Taxonomy of Protista

A modern non-hierarchical interpretation of the phylogeny of eukaryotes, including protists

A protist (/ˈproʊtɪst/) is any eukaryotic organism (one with cells containing a nucleus) that is not an animal, plant, or fungus. The protists do not form a natural group, or clade, since they exclude certain eukaryotes with whom they share a common ancestor;^[a] but, like algae or invertebrates, the grouping is used for convenience. In some systems of biological classification, such as the popular five-kingdom scheme proposed by Robert Whittaker in 1969, the protists make up a kingdom called Protista, composed of "organisms which are unicellular or unicellular-colonial and which form no tissues".^[1][b] In the 21st century, the classification shifted toward a two-kingdom system of protists: Chromista (containing the chromalveolate, rhizarian and hacrobian groups) and Protozoa (containing excavates and all protists more closely related to animals and fungi).^[2]

The following groups contain protists. The clade Opisthokonta also contains the animals and the fungi, and the kingdom Archaeplastida also contains algae and plants.

Key to symbols used:

(P) = Paraphyletic group.

† = Extinct group.

? = Group of uncertain taxonomic position.

* = Group lacking molecular data.

[ ] = Synonyms and alternative names.

This article largely follows the efforts of the scientific community and the International Society of Protistologists to revise the taxonomy of protists in a manner that reflects their phylogeny and evolution, striving away from the use of historical paraphyletic taxa and relying exclusively on clades as the basis of the classification. The reference used for the general arrangement of groups is the publication Revisions to the Classification, Nomenclature and Diversity of Eukaryotes, published in 2019 by researcher Sina Adl and coauthors.^[3] Other studies are used for some specific groups of protists that have been revised after 2018, such as slime moulds,^[4] glaucophyte algae,^[5] arcellinid testate amoebae^[6] and planktonic foraminifera.^[7]

The following cladogram shows the relationships between the major groups of protists, as well as the kingdoms of animals, plants and fungi, according to the most recent phylogenetic analyses.^{[8][9][10][11][12]}

• Apusomonadida^[c] Karpov & Mylnikov 1989 [Apusomonadidae Karpov & Mylnikov 1989; Thecomonadea Cavalier-Smith 1993 emend. 2013]. Amastigomonas, Multimonas, Podomonas, Catacumbia, Cavaliersmithia.^[16]
  • Apusomonadinae Cavalier-Smith 2010. Apusomonas, Manchomonas.
  • Thecamonadinae Larsen & Patterson 1990. Chelonemonas, Karpovia, Singekia, Thecamonas.

• Breviatea^[c] Cavalier-Smith 2004 [Breviatida Cavalier-Smith 2004; Breviatidae Cavalier-Smith 2013]. Breviata, Lenisia, Pygsuia, Subulatomonas.

• Nucletmycea Brown et al. 2009 [Holomycota Liu et al. 2009]
  • Rotosphaerida Rainer 1968 [Cristidiscoidida Page 1987, Cavalier-Smith 1993, 1998; Nucleariidae Patterson 1983, 1999]. Fonticula, Nuclearia, Parvularia, Pompholyxophrys, Lithocolla, ?Vampyrellidium*, ?Elaeorhanis*, ?Pinaciophora*, ?Rabdiophrys*, ?Rabdiaster*, ?Thomseniophora*.^[17]
  • Fungi R.T. Moore 1980. Excluded from protists.
• Holozoa Lang et al. 2002. Incertae sedis: Tunicaraptor Tikhonenkov, Mikhailov, Hehenberger, Karpov, Prokina, Esaulov, Belyakova, Mazei, Mylnikov, Aleoshin & Keeling 2020,^[11] †Bicellum Strother & Wellman 2021.^[18]
  • Ichthyosporea^[d] Cavalier-Smith 1998 [Mesomycetozoea Mendoza et al. 2002]
    • Dermocystida Cavalier-Smith 1998 [Rhinosporidaceae Mendoza et al. 2001]. Amphibiocystidium, Amphibiothecum, Chromosphaera, Dermocystidium, Rhinosporidium, Sphaerothecum.
    • Ichthyophonida Cavalier-Smith 1998 [Ichthyophonae Mendoza et al. 2001; Amoebidiidae Reeves 2003]. Abeoforma, Amoebidium, Anurofeca, Astreptonema, Caullerya, Creolimax, Eccrinidus, Enterobryus, Enteropogon, Ichthyophonus, Palavascia, Pseudoperkinsus, Psorospermium, Sphaeroforma.
  • Pluriformea^[d] Hehenberger et al. 2017
    • Corallochytrium Raghu-Kumar 1987
    • Syssomonas^[d] Tikhonenkov, Hehenberger, Mylnikov & Keeling 2017
  • Filasterea Shalchian-Tabrizi et al. 2008. Capsaspora, Ministeria, Pigoraptor, Txikispora.^[19]
  • Choanozoa Brunet & King 2017 [Choanozoa Cavalier-Smith et al. 1991 (P)]^[e]
    • Choanoflagellata Kent 1880–1882 [Craspedomonadina Stein 1878; Craspedomonadaceae Senn 1900; Craspedophyceae Chadefaud 1960; Craspédomonadophycidées Bourrelly 1968; Craspedomonadophyceae Hibberd 1976; Choanomonadea Krylov et al. 1980; Choanoflagelliida Lee, Hutner & Bovee 1985; Choanoflagellatea Cavalier-Smith 1997 emend. Cavalier-Smith 1998; Choanomonada Adl et al. 2005].
      • Craspedida Cavalier-Smith 1997, emend. Nitsche et al. 2011
        • Salpingoecidae Kent 1880–1882, emend. sensu Nitsche et al. 2011. Astrosiga, Aulomonas, Barroeca,^[20] Choanoeca, Cladospongia, Codonocladium, Codonosigopsis, Codosiga [Codonosiga], Desmarella [Codonodesmus; Kentrosiga], Dicraspedella, Diploeca, Diplosiga, Diplosigopsis, Hartaetosiga, Kentia, Lagenoeca, Microstomoeca, Monosiga, Mylnosiga, Pachysoeca, Proterospongia, Salpingoeca, Salpingorhiza, Sphaeroeca, Stagondoeca, Stelexomonas, Stylochromonas.
      • Acanthoecida Cavalier-Smith 1997, emend. Nitsche et al. 2011
        • Acanthoecidae Norris 1965, emend. sensu Nitsche et al. 2011. Acanthoeca, Enibas,^[21] Helgoeca, Polyoeca, Savillea.
        • Stephanoecidae Leadbeater 2011. Acanthocorbis, Amoenoscopa, Apheloecion, Bicosta, Calliacantha, Calotheca, Campanoeca, Campyloacantha, Conion, Cosmoeca, Crinolina, Crucispina, Diaphanoeca, Didymoeca, Kakoeca, Monocosta, Nannoeca, Parvicorbicula, Platypleura, Pleurasiga, Polyfibula, Saepicula, Saroeca, Spinoeca, Spiraloecion, Stephanacantha, Stephanoeca, Syndetophyllum.
    • Metazoa Haeckel 1874, emend. Adl et al. 2005 [Animalia Linnaeus 1758; Eumetazoa Bütschli 1910]. Excluded from protists.

Incertae sedis Amoebozoa: Belonocystis, Boveella, Biomyxa, Corallomyxa, Gibbodiscus, Hartmannia, Malamoeba, Malpighamoeba, Microglomus, Oscillosignum, Pseudothecamoeba, Rhabdamoeba, Schoutedamoeba, Stereomyxa, Subulamoeba, Thecochaos, Triaenamoeba, Unda.^[3]

• Corycida Kang et al. 2017 ["Corycidia"]^[23]
  • Trichosida Möbius 1889 [Trichosphaeriidae Sheehan & Banner 1973]. Trichosphaerium.
  • Microcoryciidae de Saedeleer 1934. Amphizonella, Diplochlamys, Trichosphaerium [Atrichosa], Microcorycia*, Parmulina*, Penardochlamys*, Zonomyxa*.^[f]
• Echinamoebida Cavalier-Smith 2004.
  • Echinamoebidae Page 1975. Echinamoeba, Micriamoeba.
  • Vermamoebidae Cavalier-Smith & Smirnov 2011. Vermamoeba.
• Elardia Kang et al. 2017^[23]
  • Leptomyxida Pussard & Pons 1976 sensu Page 1987
    • Leptomyxidae Pussard & Pons 1976. Leptomyxa.
    • Rhizamoebidae Smirnov et al. 2016. Rhizamoeba.^[24]
    • Flabellulidae Bovee 1970. Flabellula [incl. Paraflabellula].
    • Gephyramoebidae Pussard & Pons 1976. Gephyramoeba.^[24]
  • Arcellinida Kent 1880. Incertae sedis genera: Acipyxis, Apolimia, Argynnia, Armipyxis, Conicocassis, Cornuapyxis, Ellipsopyxella, Ellipsopyxis, Erugomicula, Frenopyxis, Geamphorella, Geoplagiopyxis, Geopyxella, Hoogenraadia, Jungia, Lagenodifflugia, Lamptopyxis, Lamptoquadrula, Leptochlamys, Maghrebia, Meisterfeldia, Microquadrula, Nabranella, Oopyxis, Paracentropyxis, Paraquadrula, Pentagonia, Physochila, Planhoogenraadia, Pomoriella, Pontigulasia, Prantlitina,^[25] Proplagiopyxis, Protoplagiopyxis, Protocucurbitella, Pseudawerintzewia, Pseudonebela, Schoenbornia, Sexangularia, Suiadifflugia, Trigonopyxis, Wailesella.^[6]
    • Phryganellina Bovee 1985
      • Phryganellidae Jung 1942. Phryganella.
      • Cryptodifflugiidae Jung 1942. Cryptodifflugia.^[26]
    • Organoconcha Lahr et al. 2019
      • Microchlamyiidae Ogden 1985. Microchlamys, Spumochlamys, Pyxidicula.
    • Glutinoconcha Lahr et al. 2019
      • Volnustoma Lahr et al. 2019
        • Heleoperidae Jung 1942. Heleopera.
      • Hyalospheniformes Lahr et al. 2019
        • Hyalospheniidae Schultze 1877 emend. Kosakyan et al. 2012. Alabasta, Alocodera, Apodera, Certesella, Cornutheca, Gibbocarina, Hyalosphenia, Longinebela, Mrabella, Nebela, Padaungiella, Planocarina, Porosia, Quadrulella.
      • Excentrosoma Lahr et al. 2019
        • Centropyxidae Jung 1942 [includes Plagiopyxidae]. Awerinzewia, Bullinularia, Centropyxis, Golemanskia,^[6] Plagiopyxis.
      • Cylindrothecina González-Miguéns, Todorov, Blandenier, Porfirio-Sousa, Ribeiro, Ramos, Lahr & Lara 2022
        • Cylindrifflugiidae González-Miguéns, Todorov, Blandenier, Porfirio-Sousa, Ribeiro, Ramos, Lahr & Lara 2022.^[6] Cylindrifflugia.
      • Longithecina Lahr et al. 2019
        • Difflugiidae Wallich 1864. Difflugia, Zivkovicia.
        • Lesquereusiidae Jung 1942. Lesquereusia.
      • Sphaerothecina Kosakyan et al. 2016
        • Arcellidae Ehrenberg 1843. Arcella, Galeripora.
        • Netzeliidae Kosakyan et al. 2016. Cucurbitella, Cyclopyxis, Netzelia
  • Euamoebida Lepşi 1960 sensu Smirnov et al. 2011^[27]
    • Amoebina Cavalier-Smith 2016
      • Amoebidae Ehrenberg 1838 Page 1987. Amoeba, Chaos, Polychaos, Parachaos, Trichamoeba, Deuteramoeba, Hydramoeba
      • Hartmannellidae Volkonsky 1931. Cashia, Copromyxa, Copromyxella, Glaeseria, Hartmannella, Ptolemeba, Saccamoeba
    • Nolandina Cavalier-Smith 2016^[27]
      • Nolandellidae Cavalier-Smith 2011, Lahr & Katz 2011. Nolandella.

• Variosea^[g] Cavalier-Smith 2004
  • Angulamoeba Berney, Bass & Geisen 2015
  • Arboramoeba Berney, Bass & Geisen 2015
  • Darbyshirella Berney, Bass & Geisen 2015
  • Dictyamoeba Berney, Bass & Geisen 2015
  • Ischnamoeba Berney, Bass & Geisen 2015
  • Heliamoeba Berney, Bass & Geisen 2015
  • Filamoeba Page 1967
  • Phalansterium Cienkowski 1870.
  • Flamellidae Lahr & Katz in Lahr et al. 2011.^[28] Flamella, Telaepolella.
  • Protosteliida Olive & Stoianovitch 1966, sensu Shadwick & Spiegel in Adl et al. 2012. Protostelium [incl. Planoprotostelium].
  • Fractovitellida Lahr et al. 2011, sensu Kang et al. 2017
    • Acramoebidae Smirnov, Nassonova & Cavalier-Smith 2008. Acramoeba.
    • Schizoplasmodiidae Shadwick & Spiegel in Adl et al. 2012. Ceratiomyxella, Nematostelium, Schizoplasmodium.
    • Soliformoviidae Lahr & Katz 2011. Soliformovum, Grellamoeba
  • Cavosteliida Shadwick & Spiegel in Adl et al. 2012. Cavostelium, Schizoplasmodiopsis, Tychosporium.
  • Holomastigida Lauterborn 1895. Artodiscus, Multicilia.
• Eumycetozoa Zopf 1884 sensu Kang et al. 2017 [Mycetozoa de Bary 1859 ex Rostafinski 1873; Macromycetozoa Fiore-Donno 2010]
  • Dictyostelia Lister 1909 sensu Sheikh et al. 2018 [Dictyosteliomycetes Doweld 2001]. Acytostelium, Cavenderia, Coremiostelium, Dictyostelium, Heterostelium, Polysphondylium, Raperostelium, Rostrostelium, Speleostelium, Tieghemostelium, Synstelium, ?Coenonia.
  • Protosporangiida Shadwick & Spiegel in Adl et al. 2012 [Ceratiomyxea Leontyev, Stephenson, Novozhilov & Shchepin 2019; Ceratiomyxomycetes D. Hawksw., B. Sutton & Ainsw. 2019]^[4]
    • Ceratiomyxa Schroeter 1889
    • Protosporangiidae Spiegel in Adl et al. 2012. Clastostelium, Protosporangium.
  • Myxogastria Macbride 1899 [Myxogastrea Cavalier-Smith 1993; Myxomycetes Link 1833, sensu Haeckel 1866]
    • Lucisporomycetidae [Lucisporinia Leontyev, Stephenson, Novozhilov & Shchepin 2019;^[4] Lucisporidia Cavalier-Smith 2013]. Incertae sedis genera: Arcyriatella, Calonema, Minakatella, Trichioides.
      • Cribariidia Leontyev, Stephenson, Novozhilov & Shchepin 2019^[4]
        • Cribariales T. Macbr. 1922
          • Cribariaceae Corda 1838. Cribaria, Lindbladia, Licaethalium.
      • Trichiidia Leontyev, Stephenson, Novozhilov & Shchepin 2019^[4]
        • Reticulariales Leontyev, Stephenson, Novozhilov & Shchepin 2019^[4]
          • Reticulariaceae Chevall. 1842. Alwisia, Lycogala, Reticularia, Tubifera.
        • Liceales E. Jahn 1928
          • Liceaceae Chevall. 1826. Licea, Listerella.
        • Trichiales T. Macbr. 1922
          • Dianemataceae T. Macbr. 1922. Calomyxa, Dianema, Dictydiaethalium, Prototrichia.
          • Trichiaceae Chevall. 1826 sensu Martin & Alexopoulos 1969. Hemitrichia [incl. Trichia decipiens], Arcyria [incl. Arcyodes], Perichaena, Trichia [incl. Cornuvia, Metatrichia, Oligonema].
    • Columellomycetidae [Collumellinia Leontyev, Stephenson, Novozhilov & Shchepin 2019;^[4] Columellidia Cavalier-Smith 2015]. Incertae sedis genera: Diachea, Echinosteliopsis, Leptoderma, Paradiachea, Protophysarum, Trabrooksia, Willkommlangea.
      • Echinosteliidia Leontyev, Stephenson, Novozhilov & Shchepin 2019^[4]
        • Echinosteliales G. W. Martin 1961
          • Echinosteliaceae Rostaf. ex Cooke 1877. Barbeyella, Echinostelium [incl. Semimorula].
      • Stemonitidia Leontyev, Stephenson, Novozhilov & Shchepin 2019^[4]
        • Clastodermatales Leontyev, Stephenson, Novozhilov & Shchepin 2019^[4]
          • Clastodermataceae Alexop. & T.E. Brooks 1971. Clastoderma.
        • Meridermatales Leontyev, Stephenson, Novozhilov & Shchepin 2019^[4]
          • Meridermataceae Leontyev, Stephenson, Novozhilov & Shchepin 2019. Meriderma.
        • Stemonitidales T. Macbr. 1922 em. Leontyev, Stephenson, Novozhilov & Shchepin 2019
          • Stemonitidaceae Fr. 1829 em. Leontyev, Stephenson, Novozhilov & Shchepin 2019. Macbrideola, Stemonitis, Symphytocarpus.
          • Amaurochaetaceae Rostaf. ex Cooke 1877 em. Leontyev, Stephenson, Novozhilov & Shchepin 2019. Comatricha, Stemonaria, Stemonitopsis, Amaurochaete, Brefeldia, Enerthenema, Paradiacheopsis.
        • Physarales T. Macbr. 1922
          • Tasmaniomyxa umbilicata Lloyd et al. 2023^[29]
          • Lamprodermataceae T. Macbr. 1899 em. Leontyev, Stephenson, Novozhilov & Shchepin 2019. Lamproderma [incl. Dichaeopsis, Colloderma, Elaeomyxa], ?Collaria.
          • Didymiaceae Rostaf. ex Cooke 1877 – Diderma, Didymium, Lepidoderma, Mucilago.
          • Physaraceae Chevall. 1826. Craterium, Leocarpus, Fuligo, Physarum, Physarella, Physarina, Kelleromyxa, Badhamia.
• Cutosea Cavalier-Smith 2016 [Squamocutida Cavalier-Smith 2016]
  • Squamamoebidae Cavalier-Smith 2016. Armaparvus, Squamamoeba.
  • Sapocribridae Cavalier-Smith 2016. Sapocribrum.
  • Idionectidae Hess & Simpson 2019. Idionectes.^[30]
• Archamoebea Cavalier-Smith 1983, sensu Cavalier-Smith 2004
  • Tricholimacidae Cavalier-Smith 2012. Tricholimax.
  • Entamoebidae Chatton 1925. Entamoeba.
  • Rhizomastixidae Ptáčková et al. 2013. Rhizomastix.
  • Mastigamoebida Frenzel 1897, sensu Cavalier-Smith 2013.^[h] Endamoeba, Endolimax, Iodamoeba, Mastigamoeba, Mastigina.
  • Pelobiontida Page 1976, sensu Cavalier-Smith 2013 [Pelomyxidae Schulze 1877]. Mastigella, Pelomyxa

• Flabellinia Smirnov et al. 2005
  • Dermamoebida Cavalier-Smith 2004
    • Dermamoebidae Cavalier-Smith & Smirnov 2011. Dermamoeba, Paradermamoeba, ?Mycamoeba,^[i] Coronamoeba.^[32]
    • Mayorellidae Schaeffer 1926. Mayorella.
  • Thecamoebida^[h] Schaeffer 1926, sensu Smirnov & Cavalier-Smith 2011. Sappinia, Stenamoeba, Stratorugosa,^[33] Thecamoeba, Thecochaos.^[34]
  • Dactylopodida^[h] Smirnov et al. 2005 sensu Kang et al. 2017. Cunea, ?Janickina,* Korotnevella, Neoparamoeba, Paramoeba, Pseudoparamoeba, Vexillifera.
  • Vannellida Smirnov et al. 2005 [Vannellidae Bovee 1979]. Clydonella, Lingulamoeba, Paravannella, Pessonella*,^[j] Ripella, Vannella.
• Stygamoebida^[k] Smirnov & Cavalier-Smith in Smirnov et al. 2011 (P). Stygamoeba, Vermistella.
• Centramoebia Cavalier-Smith et al. 2016^[27]
  • Acanthopodida^[h] Page 1976 [Centramoebida Rogerson & Patterson 2002, sensu Tice et al. 2016^[35]]. Acanthamoeba, Balamuthia, Luapeleamoeba, Protacanthamoeba, Dracoamoeba, Vacuolamoeba.
  • Himatismenida^[h] Page 1987. Cochliopodium, Ovalopodium, Parvamoeba.
  • Pellitida^[h] Smirnov & Cavalier-Smith 2011, sensu Kang et al. 2017. Endostelium, Gocevia, Paragocevia*, Pellita.

• Microheliella maris^[l] Cavalier-Smith 2012
• Telonemia^[m] Shalchian-Tabrizi 2006 [Telonemidae Cavalier-Smith 1993]. Arpakorses,^[36] Lateronema, Telonema.
• Provora Tikhonenkov et al. 2022^[10]
  • Nibbleridia Tikhonenkov et al. 2022. Nibbleromonas, Ubysseya.
  • Nebulidia Tikhonenkov et al. 2022. Nebulomonas, Ancoracysta.

• Glaucophyta Skuja 1954 [Glaucocystaceae West 1904; Glaucocystophyta Kies and Kremer 1986].^[5] Incertae sedis Glaucophyta: ?Archaeopsis, ?Chalarodora, ?Glaucocystopsis, ?Peliaina, ?Strobilomonas.
  • Cyanophorales Kies & Kremer 2006. Cyanophora.
  • Glaucocystales Bessey 1907. Glaucocystis.
  • Gloeochaetales Bessey 1907. Cyanoptyche, Gloeochaete.
• Picozoa Seenivasan et al. 2013 [Picobiliphytes Not et al. 2007]. Picomonas.^[n]
• Rhodelphidia Gawryluk et al. 2019. Rhodelphis.^[38]
• Rhodophyceae Thuret 1855, emend. Rabenhorst 1863 [Rhodophyta Wettstein 1901; Rhodoplantae Saunders and Hommersand 2004 emend. Adl et al. 2005]
• Chloroplastida Adl et al. 2005 [Viridiplantae Cavalier-Smith 1981; Chlorobionta Jeffrey 1982, emend. Bremer 1985, emend. Lewis and McCourt 2004; Chlorobiota Kendrick and Crane 1997]

Stramenopiles incertae sedis:

• Environmental clades MAST-21, MAST-25 Massana et al. 2014
• Platysulcidae Shiratori, Nakayama & Ishida 2015. Platysulcus.
• Kaonashiidae Weston, Eglit & Simpson 2023. Kaonashia.^[39]

• Opalozoa Cavalier Smith 1991, emend. 2006. Incertae sedis: Cantina, Rictus, environmental clades MAST-16, MAST-22 and MAST-24 Massana et al. 2014.
  • Placidozoa Cavalier-Smith 2013
    • Placididea Moriya, Nakayama & Inouye 2002. Allegra, Haloplacidia, Pendulomonas, Placidia, Placilonga, Suigetsumonas, Wobblia.^[40]
    • Nanomonadea Cavalier-Smith 2012 [clade MAST-3]. Incisomonas, Solenicola.
    • Opalomonadea Cavalier-Smith 2013 [clade MAST-12]. No described species.
    • Opalinata Wenyon 1926, emend. Cavalier-Smith 1997 [Slopalinida Patterson 1985]
      • Proteromonadea Grassé 1952. Karotomorpha, Proteromonas.
      • Opalinea Wenyon 1926. Cepedea, Opalina, Protoopalina, Protozelleriella, Zelleriella.
      • Blastocystis Alexeieff 1911
  • Bicosoecida Grassé 1926, emend. Karpov 1998. Adriamonas, Anoeca, Bicosoeca, Caecitellus, Cafeteria, Cafileria,^[41] Cyathobodo, Filos, Halocafeteria, Nanum, Paramonas, Pseudobodo, Pseudodendromonas, Otto, Regin.^[42]
• Sagenista Cavalier-Smith 1995. Incertae sedis: environmental clades MAST-4, MAST-7, MAST-8, MAST-9, MAST-10, MAST-11 and MAST-20 Massana et al. 2014.
  • Labyrinthulomycetes Dick 2001
    • Amphitremida Poche 1913, emend. Gomaa et al. 2003. Amphitrema, Archerella, Diplophrys, Paramphitrema.
    • Amphifilida Cavalier-Smith 2012. Amphifila, Fibrophrys, Sorodiplophrys.
    • "Oblongichytrida" Bennett et al. 2017. Oblongichytrium.
    • Labyrinthulida Doffein 1901. Aplanochytrium, Labyrinthula, Stellarchytrium.
    • Thraustochytrida Sparrow 1943. Althornia, Aurantiochytrium, Botryochytrium, Japanochytrium, Monorhizochytrium, Parietichytrium, Phycophthorum,^[43] Schizochytrium, Sicyoidochytrium, Thraustochytrium, Ulkenia.
  • Pseudophyllomitidae Shiratori et al. 2016 [clade MAST-6].^[44] Pseudophyllomitus.

• Gyrista incertae sedis: environmental clades MAST-1, MAST-2 and MAST-23 Massana et al. 2014.
• Pseudofungi Cavalier-Smith 1986 [Heterokontimycotina M.W. Dick 1976]
  • Bigyromonadea Cavalier-Smith 1998^[45]
    • Developea Karpov & Aleoshin 2016. Cubaremonas, Develocanicus, Develocauda, Developayella, Develorapax, Mediocremonas.
    • Pirsoniales Cavalier-Smith 1998 emend. Prokina et al. 2024.^[46] Bordeauxia, Bullionia, Feodosia, Koktebelia, Noirmoutieria, Pirsonia.
  • Hyphochytriales Sparrow 1960. Anisolpidium, Canteriomyces.
    • Anisolpidiaceae Karling 1943, emend. Dick 2001
    • Hyphochytridiomycetaceae Fischer 1892, emend. Karling 1939. Hyphochytrium.
    • Rhizidiomycetaceae Karling 1943. Latrostium, Rhizidiomyces, Rhizidiomycopsis.
  • Oomycetes Winter 1897, emend. Dick 1976 [Peronosporomycetes Dick 2001]. Incertae sedis genera: Atkinsiella, Ciliomyces, Crypticola, Ectrogella, Eurychasma, Halodaphnea, Haliphthoros, Haptoglossa, Lagena, Lagenisma, Olpidiopsis, Pontisma, Pythiella, Rozellopsis, Sirolpidium.
    • Saprolegnialean lineage Lara in Adl et al. 2019. Achlya, Aphanomyces, Aplanopsis, Apodachlya, Aquastella, Geolegnia, Leptomitus, Newbya, Pythiopsis, Protoachlya, Salisapilia, Saprolegnia, Thraustotheca.
    • Peronosporalean lineage Lara in Adl et al. 2019. Albugo, Bremia, Chlamydomyzium, Halophytopthora, Hyaloperonospora, Lagenidium, Myzocytiopsis, Peronospora, Plasmopara, Pythium, Pseudoperonospora, Phytophthora, Phytopythium, Pustula.
• Ochrophyta Cavalier-Smith 1986, emend. Cavalier-Smith & Chao 1996 [Heterokontophyta Guiry, R.A.Andersen & Moestrup 2023]
  • Chrysista Cavalier-Smith 1986. Incertae sedis: environmental lineages MOCH-3 and MOCH-5 Massana et al. 2014, Chrysowaernella, Aurearena.
    • SII clade
      • Olisthodiscophyceae Barcytė, Eikrem & M. Eliáš 2021.^[47] Olisthodiscus.
      • Pinguiophyceae Kawachi et al. 2003. Glossomastix, Phaeomonas, Pinguiochrysis, Pinguiococcus, Polypodochrysis.
      • Limnistia Cavalier-Smith 1996 emend. 2006
        • Chrysophyceae Pascher 1914. Incertae sedis: Chryososaccus, Chrysosphera, Cyclonexis, Lygynion, Phaeoplaca.
          • Chromulinales Pascher 1910. Chromulina, Chrysomonas.
          • Hibberdiales Andersen 1989. Hibberdia.
          • Ochromonadales Pascher 1910. Spumella, Pedospumella, Ochromonas.
          • Paraphysomonadida Scoble & Cavalier-Smith 2014. Paraphysomonas.
          • Synurales Andersen 1987. Chrysodidymus, Mallomonas, Synura, Tesselaria.
        • Eustigmatophyceae Hibberd & Leedale 1971^[48]
          • Eustigmatales Hibberd 1981
            • Paraeustigmatos Fawley, Nemcová, & Fawley 2019
            • Eustigmataceae Hibberd 1981. ?Ellipsoidion, Chlorobotrys, Eustigmatos, Pseudocharaciopsis, Vischeria.
            • Monodopsidaceae Hibberd 1981. Microchloropsis, Monodopsis, Nannochloropsis, Pseudotetraedriella.
            • Neomonodaceae Amaral et al. 2020. ?Botryochloropsis, Characiopsella, Munda, Neomonodus, Pseudellipsoidion.
          • Goniochloridales Fawley, Elias & Fawley 2013. Goniochloris, Pseudostaurastrum, Tetraedriella, Trachydiscus, Vacuoliviride.
        • Picophagea Cavalier-Smith 2006 emend. 2017^[49] [Synchromophyceae S.Horn & C.Wilhelm 2007]. Chlamydomyxa, Chrysopodocystis, Guanochroma, Leukarachnion, Picophagus, Synchroma.
    • SI clade
      • Raphidomonadea Chadefaud 1950 ex Silva 1980
        • Raphidophycidae Cavalier-Smith 2013 [Chattonellales Throndsen in Tomas 1993 emend. Yamaguchi, Nakayama, Murakami & Inouye 2010; Vacuolariales Shameel, 2001]. Chattonella, Fibrocapsa, Goniostomum, Haramonas, Heterosigma, Merotricha, Vacuolaria.
        • Raphopoda Cavalier-Smith 2013
          • Commatiida Cavalier-Smith 1997 [Commatiidae Cavalier-Smith 2013]. Commation.
          • Actinophryida^[o] Claus 1874, emend. Hartmann 1926
            • Actinosphaerina Cavalier-Smith 2013 [Actinosphaeriidae Cavalier-Smith 2013]. Actinosphaerium.
            • Actinophryina Cavalier-Smith 2013
              • Actinophryidae Dujardin 1841. Actinophrys.
              • Helioraphidae Cavalier-Smith 2013. Heliorapha.
      • PX clade
        • Chrysomerophyceae Cavalier-Smith 1995. Antarctosaccion, Chrysomeris, Chrysowaernella, Giraudyopsis, Rhamnochrysis, Tetrasporopsis.
        • Chrysoparadoxophyceae Wetherbee et al. 2019.^[51] Chrysoparadoxa.
        • Phaeophyceae Hansgirg 1886 [Kjellman 1891; Pfitzer 1894]
          • Ascoseirales Petrov 1964. Ascoseira.
          • Desmarestiales Setchell & Gardner 1925. Arthrocladia, Desmarestia (P), Himantothallus, Phaeurus.
          • Dictyotales Bory de Saint-Vincent 1828. Dictyota, Dilophus, Lobophora, Padina, Stypopodium, Taonia, Zonaria.
          • Discosporangiales Kawai et al. 2007. Choristocarpus, Discosporangium.
          • Ectocarpales Bessey 1907, emend. Silva & Reviers 2000. Adenocystis, Acinetospora, Asterocladon, Asteronema, Chordaria, Ectocarpus, Scytosiphon.
          • Fucales Bory de Saint-Vincent 1927. Ascophyllum, Bifurcaria, Cystoseira, Druvillaea, Fucus, Hormosira, Sargassum, Turbinaria.
          • Ishigeales Cho et al. 2004 [Ishigeacea Okamura 1935]. Ishige.
          • Laminariales Migula 1908. Akkesiophycus, Alaria, Chorda, Costaria, Laminaria, Lessonia, Pseudochoda.
          • Nemodermatales Parente et al. 2008. Nemoderma.
          • Onslowiales Draisma & Prud'homme van Reine 2008. Onslowia.
          • Ralfsiales Nakamura ex Lim & Kawai 2007. Lithoderma, Neoralfsia, Pseudolithoderma, Ralfsia.
          • Scytothamnales Peters & Clayton 1998. Scytothamnus, Splachnidium, Stereocladon.
          • Sphacelariales Migula 1908. Chaetopteris, Halopteris, Stypocaulon, Sphacelaria, Verosphacella.
          • Sporochnales Sauvageau 1926. Bellotia, Carpomitra, Nereia, Sporochonus, Tomaculopsis.
          • Syringodermatales Henry 1984. Syringoderma.
          • Tilopteridales Bessey 1907. Cutleria, Halosiphon, Haplospora, Phaeosiphoniella, Phyllaria, Tilopteris.
        • Phaeosacciophyceae R.A.Andersen, L.Graf & H.S.Yoon 2020^[52]
          • Phaeosaccionaceae J. Feldmann 1949. Phaeosaccion.
          • Tetrasporopsidaceae R.A.Andersen, L.Graf & H.S.Yoon 2020. Tetrasporopsis, Psammochrysis, Chrysomeris.
        • Phaeothamiophyceae Andersen & Bailey in Bailey et al. 1998
          • Phaeothamniales Bourrelly 1954, emend. Andersen & Bailey in Bailey et al. 1998. Phaeothamnion.
          • Pleurochloridales Ettl 1956. Pleurochloridella.
        • Schizocladiophyceae Henry, Okuda & Kawai 2003. Schizocladia.
        • Xanthophyceae Allorge 1930, emend. Fritsch 1935 [Heterokontae Luther 1899; Heteromonadea Leedale 1983; Xanthophyta Hibberd 1990]
          • Tribonematales Pascher 1939. Botrydium, Bumilleriopsis, Characiopsis, Chloromeson, Heterococcus, Monadus, Ophiocytium, Sphaerosorus, Tribonema, Xanthonema.
          • Vaucheriales Bohlin 1901. Vaucheria.
  • Diatomista Derelle et al. 2016, emend. Cavalier-Smith 2017 [SIII clade]. Incertae sedis: environmental clades MOCH-1, MOCH-2 and MOCH-4 Massana et al. 2014.
    • Bolidophyceae Guillou et al. 1999 [Parmales Booth & Marchant 1987]. Bolidomonas, Triparma, Tetraparma, Pentalamina.
    • Diatomeae Dumortier 1821 [Bacillariophyta Haeckel 1878]
      • Leptocylindrophytina D.G. Mann, in Adl et al. 2019
        • Leptocylindrophyceae D.G. Mann, in Adl et al. 2019. Leptocylindrus, Tenuicylindrus.
        • Corethrophyceae D.G. Mann, in Adl et al. 2019. Corethron.
      • Ellerbeckiophytina D.G. Mann, in Adl et al. 2019. Ellerbeckia.
      • Probosciophytina D.G. Mann, in Adl et al. 2019. Proboscia.
      • Melosirophytina D.G. Mann, in Adl et al. 2019. Aulacoseira, Melosira, Hyalodiscus, Stephanopyxis, Paralia, Endictya.
      • Coscinodiscophytina Medlin & Kaczmarska 2004, emend. Adl et al. 2019. Actinoptychus, Coscinodiscus, Actinocyclus, Asteromphalus, Aulacodiscus, Stellarima.
      • Rhizosoleniophytina D.G. Mann, in Adl et al. 2019. Guinardia, Rhizosolenia, Pseudosolenia.
      • Arachnoidiscophytina D.G. Mann, in Adl et al. 2019. Arachnoidiscus.
      • Bacillariophytina Medlin & Kaczmarska 2004, emend. Adl et al. 2019
        • Mediophyceae Jouse & Proshkina-Lavrenko in Medlin & Kaczmarska 2004
          • Chaetocerotophycidae Round & R.M. Crawford in Round et al. 1990, emend. Adl et al. 2019. Chaetoceros, Bacteriastrum, Dactyliosolen, Cerataulina, Hemiaulus, Eucampia, Acanthoceras, Urosolenia, Terpsinoë, Hydrosera.
          • Lithodesmiophycidae Round & R.M. Crawford in Round et al. 1990, emend. Adl et al. 2019. Lithodesmium, Lithodesmioides, Helicotheca, Bellerochea, Ditylum.
          • Thalassiosirophycidae Round & R.M. Crawford in Round et al. 1990. Thalassiosira, Lindavia, Cyclotella, Stephanodiscus, Cyclostephanos, Discostella, Bacteriosira, Skeletonema, Detonula.
          • Cymatosirophycidae Round & R.M. Crawford in Round et al. 1990. Cymatosira, Minutocellus, Papiliocellulus, Leyanella, Extubocellulus, Plagiogrammopsis, Campylosira, Brockmanniella, Pierrecomperia.
          • Odontellophycidae D. G. Mann, in Adl et al. 2019. Odontella, Triceratium, Cerataulus, Pleurosira, Pseudauliscus, Amphitetras, Trieres, Mastodiscus.
          • Chrysanthemodiscophycidae D.G. Mann, in Adl et al. 2019. Chrysanthemodiscus, Biddulphiopsis, Trigonium, Isthmia, Lampriscus, Stictocyclus, Ardissonea, Climacosphenia, Toxarium.
        • Biddulphiophyceae D. G. Mann, in Adl et al. 2019
          • Biddulphiophycidae Round and R.M. Crawford in Round et al. 1990, emend. Adl et al. 2019. Biddulphia.
          • Attheya T. West 1860
        • Bacillariophyceae Haeckel 1878, emend. Adl et al. 2019
          • Striatellaceae Kützing 1844. Striatella, Pseudostriatella.
          • Urneidophycidae Medlin 2016. (P?) Plagiogramma, Dimeregramma, Rhaphoneis, Delphineis, Psammoneis, Bleakeleya, Asterionellopsis.
          • Fragilariophycidae Round in Round, Crawford & Mann 1990, emend. Adl et al. 2019. Fragilaria, Synedra, Tabellaria, Asterionella, Diatoma, Tabularia, Cyclophora, Astrosyne, Licmophora, Rhabdonema, Grammatophora, Staurosira, Thalassionema.
          • Bacillariophycidae D.G. Mann in Round, Crawford & Mann 1990, emend. Adl et al. 2019. Eunotia, Achnanthes, Bacillaria, Nitzschia, Pseudonitzschia, Cylindrotheca, Navicula, Seminavis, Haslea, Pleurosigma, Gyrosigma, Achnanthidium, Cocconeis, Frustulia, Diploneis, Sellaphora, Pinnularia, Gomphonema, Cymbella, Didymosphenia, Phaeodactylum, Amphora, Entomoneis, Epithemia, Surirella, etc.
            • Naviculales Bessey 1907
              • Stauroneidaceae D.G. Mann in Round, Crawford & Mann 1990. Craticula, Dorofeyukea, Fistulifera, Karayevia, Madinithidium, Parlibellus, Prestauroneis, Stauroneis, Schizostauron.^[53]
    • Dictyochophyceae Silva 1980 [Silicoflagellata Lemmermann, 1901]
      • Dictyochales Haeckel 1894 [Dictyochida Borgert, 1891; Dictyochaceae Lemmermann, 1901]. Dictyocha.
      • Florenciellales Eikrem, Edvardsen & Throndsen 2007.^[54] Florenciella, Verrucophora.
      • Pedinellales Zimmermann et al. 1984 [Ciliophryida Febre-Chevalier, 1985; Actinomonadaceae Kent, 1880]. Actinomonas, Apedinella, Ciliophrys, Mesopedinella, Palatinella, Pedinella, Pseudopedinella, Pteridomonas.
      • Rhizochromulinales O'Kelly & Wujek 1994 [Rhizochromulinaceae O'Kelly & Wujek, 1994]. Rhizochromulina.
    • Pelagophyceae Andersen & Saunders 1993
      • Pelagomonadales Andersen & Saunders 1993. Aureococcus, Pelagococcus, Pelagomonas.
      • Sarcinochrysidales Gayral & Billard 1977
        • Sarcinochrysidaceae Gayral & Billard 1977. Ankylochrisis, Arachnochrysis, Aureoscheda, Aureoumbra, Nematochrysopsis, Pelagospilus, Pulvinaria, Sarcinochrysis, Sargassococcus.
        • Chrysocystaceae M.Melkonian, H.S.Yoon & R.A.Andersen 2018.^[55] Chrysocystis, Chrysoreinhardia, Sungminbooa.
      • Plocamiomonadales Daugbjerg & Lovejoy 2024. Plocamiomonas.^[56]

• Colponemida Cavalier-Smith 1993 emend. Adl et al. 2019 (P)
  • Colponemidia Tikhonenkov et al. 2014. Colponema.
  • Acavomonidia Tikhonenkov et al. 2014. Acavomonas.
  • Neocolponema Gigeroff et al. 2023^[57]
  • Loeffela Gigeroff et al. 2023^[57]
  • Palustrimonas Patterson & Simpson 1996

• Colpodellida Cavalier-Smith 1993, emend. Adl et al. 2005, 2019 ["chrompodellids" Janouškovec et al. 2015;^[59] Chromeridophyta R.B.Moore et al., 2008; Colpodellophyceae Molinari & Guiri 2023; Chromerida Guiry 2024].^[60] Incertae sedis: Piridium.^[61]
  • Vitrellaceae Oborník & Lukeš 2012. Vitrella.
  • Colpodellaceae Adl et al. 2019 [Colpodellidae Simpson & Patterson 1996]. Colpodella, Chilovora, Voromonas.
  • Chromeraceae Oborník & Lukeš 2012. Chromera.
  • Alphamonaceae Adl et al. 2019. Alphamonas.
• Perkinsozoa Norén & Moestrup in Norén et al 1999 [Perkinsea Levine 1978]. Incertae sedis genus: Phagodinium, Rastrimonas.^[p]
  • Maranthos Alacid & Reñé 2021^[63]
  • Pararosariidae Jeon & Park 2021. Pararosarium.^[64]
  • Parviluciferaceae Reñé & Alacid 2017. Dinovorax, Parvilucifera, Snorkelia,^[65] Tuberlatum.^[66]
  • Perkinsidae Levine 1978. Perkinsus.
  • Xcellidae Freeman, Fuss, Kristmundsson, Keeling, Shalchian-Tabrizi & Bass 2017 em. Karlsbakk, Nystøyl, Plarre & Nylund 2021. Cryoxcellia,^[67] Gadixcellia, Notoxcellia,^[68] Salmoxcellia,^[69] Xcellia.
• Dinoflagellata Bütschli 1885, emend. Fensome et al. 1993, emend. Adl et al. 2005. Incertae sedis genera: free-living (Adenoides, Akashiwo, Amphidiniella, Ankistrodinium, Apicoporus, Archaeosphaerodiniopsis, Bispinodinium, Bysmatrum, Cabra, Cladopyxis, Crypthecodinium, Cucumeridinium, Dactylodinium, Dicroerisma, Gloeodinium, Grammatodinium, Gynogonadinium, Gyrodiniellum, Halostylodinium, Heterodinium, Moestrupia, Paragymnodinium, Phytodinium, Plagiodinium, Planodinium, Pileidinium, Pseudadenoides, Pseudothecadinium, Pyramidodinium, Rhinodinium, Roscoffia, Sabulodinium, Sphaerodinium, Spiniferodinium, Testudodinium, Thecadinium, Thecadiniopsis, Togula) and parasitic Blastodiniales Chatton 1906 [no longer valid] (Amyloodinium, Apodinium, Cachonella, Caryotoma, Crepidoodinium, Haplozoon, Oodinium, Myxodinium, Piscinoodinium, Protoodinium, Rhinodinium, Schyzochitriodinium, Stylodinium).
  • Psammosa Okamoto, A. Horák & Keeling 2012^[70][71]
  • Oxyrrhis Dujardin 1841 [Oxyrrhinaceae Sournia 1984]^[71]
  • Eleftheros Tikhonenkov, Hehenberger & Keeling 2023^[71]
  • Ichthyodinida Cavalier-Smith 2018 [environmental Marine Alveolate Group I]^[71]
    • Hobagellidae Yoo, Kim & Wayne Coats 2024. Hobagella.^[72]
    • Euduboscquellidae Coats & Bachvaroff 2012. Euduboscquella, Dogelodinium, Keppenodinium.
    • Ichthyodiniidae Cavalier-Smith 2018. Ichthyodinium.
  • Syndiniales Loeblich III 1976. Incertae sedis: Ellobiopsidae (Ellobiopsis, Thalassomyces).
    • Amoebophryidae Cachon 1964 [environmental Marine Alveolate Group II]. Amoebophrya.
    • Syndinidae Chatton 1910 [environmental Marine Alveolate Group IV]. Hematodinium, Syndinium, Solenodinium.
    • Sphaeriparaceae Loeblich III 1970. Atlanticellodinium, Sphaeripara.
  • Noctilucales Haeckel 1894 [Noctiluciphyceae Fensome et al. 1993]. Abedinium, Cachonodinium, Craspedotella, Cymbodinium, Kofoidinium, Leptodiscus, Noctiluca, Petalodinium, Pomatodinium, Scaphodinium, Spatulodinium.
  • Dinophyceae Pascher 1914
    • Gymnodiniphycidae Fensome et al. 1993
      • Gymnodiniales F. Stein 1878, emend. G. Hansen & Moestrup in Daugbjerg et al. 2000 sensu stricto. Barrufeta, Chytriodinium, Dissodinium, Erythropsidinium, Greuetodinium, Gymnodinium, Lepidodinium, Nematodinium, Nusuttodinium, Pellucidodinium, Polykrikos, Proterythropsis, Wangodinium,^[73] Warnowia.
      • Amphidinium Claparède & Lachmann 1859, emend. Flø Jørgensen et al. 2004 sensu stricto
      • Gyrodinium Kofoid & Swezy 1921, emend. G. Hansen & Moestrup in Daugbjerg et al. 2000 sensu stricto
      • Kareniaceae Bergholtz et al. 2005. Brachidinium, Karenia, Karlodinium, Takayama.
      • Ceratoperidiniaceae Loeblich III 1980, emend. Reñé & de Salas 2013. Ceratoperidinium, Kirithra.
      • Torodiniales Boutrup, Moestrup & Daugbjerg 2016. Kapelodinium, Torodinium.
      • Levanderina Moestrup et al. 2014
      • Margalefidinium F. Gómez, Richlen & D.M. Anderson 2017
      • Cochlodinium F. Schütt emend. F. Gómez, Richlen & D.M. Anderson 2017 sensu stricto
      • Ptychodiscales Fensome et al. 1993. Achradina, Amphilothus, Balechina, Ptychodiscus, Sclerodinium.
      • Borghiellaceae Moestrup, Lindberg, & Daugbjerg 2009. Baldinia, Borghiella.
      • Tovelliaceae Moestrup et al. 2005. Bernardinium, Esoptrodinium, Jadwigia, Tovellia.
      • Suessiaceae Fensome et al. 1993, emend. Moestrup et al. 2009. Ansanella, Asulcocephalium, Biecheleria, Biecheleriopsis, Leiocephalium, Pelagodinium, Polarella, Prosoaulax, Protodinium, Symbiodinium, Yihiella.
    • Peridiniphycidae Fensome et al. 1993
      • Gonyaulacales Taylor 1980. Alexandrium, Amylax, Ceratium, Ceratocorys, Coolia, Fukuyoa, Fragilidium, Gambierdiscus, Goniodoma, Gonyaulax, Lingulodinium, Ostreopsis, Pentaplacodinium, Peridiniella, Protoceratium, Pyrocystis, Pyrodinium, Pyrophacus, Tripos.
      • Peridiniales Haeckel 1894. Amphidiniopsis, Archaeperidinium, Blastodinium*, Diplopelta, Diplopsalis, Diplopsalopsis, Herdmania, Niea, Oblea, Palatinus, Parvodinium, Peridinium, Peridiniopsis, Preperidinium, Protoperidinium, Qia, Vulcanodinium.
      • Thoracosphaeraceae Schiller 1930. Aduncodinium, Amyloodinium, Apocalathium, Blastodinium, Chimonodinium, Cryptoperidiniopsis, Duboscquodinium, Ensiculifera, Laciniporus,^[74] Leonella, Luciella, Naiadinium, Paulsenella, Pentapharsodinium, Pfiesteria, Scrippsiella, Stoeckeria, Theleodinium, Thoracosphaera, Tintinnophagus, Tyrannodinium.
      • Podolampadaceae Lindemann 1928. Blepharocysta, Gaarderiella, Heterobractum, Lissodinium, Mysticella, Podolampas.
      • Kryptoperidiniaceae Lindemann 1925 ["dinotoms"]. Blixaea, Durinskia, Galeidinium, Kryptoperidinium, Unruhdinium, etc.
      • Heterocapsaceae Fensome et al. 1993. Heterocapsa.
      • Amphidomataceae Sournia 1984. Amphidoma, Azadinium.
      • Oxytoxaceae Lindemann 1928. Corythodinium, Oxytoxum.
      • Centrodiniaceae Hernández-Becerril 2010. Centrodinium.
    • Dinophysales Kofoid 1926. Amphisolenia, Citharistes, Dinofurcula, Dinophysis, Histioneis, Latifascia, Metadinophysis, Metaphalacroma, Ornithocercus, Oxyphysis, Parahistioneis, Phalacroma, Pseudophalacroma, Sinophysis, Triposolenia.
    • Prorocentrales Lemmermann 1910. Mesoporus, Prorocentrum.
• Squirmida Cavalier-Smith 2014. Digyalum, Filipodium, Platyproteum.^[75][76]
• Apicomplexa Levine 1980, emend. Adl et al. 2005. Incertae sedis genera: Aggregata^[q] Frenzel 1885, Christalloidophora Dehorne 1934, Dobellia* Ikeda 1914, Echinococcidium* Porchet 1978, Globidiellum* Brumpt 1913, Joyeuxella* Brasil 1902, Rhabdospora* Laguesse 1906, Spermatobium* Eisen 1895, Spiriopsis* Arvy & Peters 1972, Spirogregarina* Wood & Herman 1943, Toxocystis* Léger & Duboscq 1910, Trophosphaera* Le Calvez 1939.
  • ?Agamococcidiorida Levine 1979. Gemmocystis*, Rhytidocystis.
  • ?Protococcidiorida Kheisin 1956. Angeiocystis*, Coelotropha*, Grellia*, Eleutheroschizon*, Mackinnonia*, Myriosporides*, Myriospora*, Sawayella*.
  • Aconoidasida Mehlhorn et al. 1980 [Hematozoa Vivier 1982] (P)
    • Haemospororida Danilewsky 1885. Dionisia*, Haemocystidium, Haemoproteus, Hepatocystis, Leucocytozoon, Mesnilium*, Nycteria, Parahaemoproteus, Plasmodium, Polychromophilus, Rayella*, Saurocytozoon*.
    • Piroplasmorida Wenyon 1926. Anthemosoma*, Babesia, Cytauxzoon, Echinozoon*, Haemohormidium*, Sauroplasma*, Serpentoplasma*, Theileria.
    • Nephromycida Cavalier-Smith 1993, emend. Adl et al. 2019. Nephromyces, Cardiosporidium.
  • Conoidasida Levine 1988 (P)
    • Coccidia Leuckart 1879 (P)
      • Adeleorina Léger 1911. Adelea*, Adelina, Babesiosima*, Bartazoon*, Chagasella*, Cyrilia*, Dactylosoma, Desseria*, Ganapatiella*, Gibbsia*, Haemogregarina, Haemolivia, Hepatozoon, Ithania*, Karyolysus, Klossia, Klossiella*, Legerella*, Orcheobius*, Rasajeyna*.
      • Eimeriorina Léger 1911. Atoxoplasma, Barrouxia*, Besnoitia, Caryospora, Caryotropha, Choleoeimeria, Cyclospora, Cystoisospora, Defretinella*, Diaspora*, Dorisa*, Dorisiella*, Eimeria, Elleipsisoma*, Goussia, Hammondia, Hyaloklossia, Isospora, Lankesterella, Mantonella*, Merocystis, Neospora, Nephroisospora, Ovivora*, Pfeifferinella, Pseudoklossia, Sarcocystis, Schellackia, Selenococcidium*, Selysina*, Spirocystis*, Toxoplasma, Tyzzeria*, Wenyonella*.
    • Gregarinasina Dufour 1828 (P). Incertae sedis genera: Digyalum Koura et al. 1990, Exoschizon Hukui 1939.
      • Archigregarinorida Grassé 1953 (P). Meroselenidium, Merogregarina, Selenidium, Selenocystis, Veloxidium.
      • Eugregarinorida Léger 1900 (P). Apolocystis*, Amoebogregarina, Ancora, Ascogregarina, Asterophora, Blabericola, Caliculium, Cephaloidophora, Colepismatophila, Cystobia*, Cystocephalus*, Difficilina, Diplauxis*, Enterocystis, Ganymedes, Geneiorhynchus, Gonospora, Gregarina, Heliospora, Hentschelia*, Hirmocystis*, Hoplorhynchus, Lankesteria, Lecudina, Leidyana, Lithocystis, Monocystella*, Monocystis, Nematopsis, Nematocystis*, Neoasterophora*, Paralecudina, Paraschneideria, Phyllochaetopterus, Pileocephalus*, Polyplicarium, Polyrhabdina, Porospora*, Prismatospora, Protomagalhaensia, Psychodiella, Pterospora, Pyxinia, Pyxinioides, Rhabdocystis*, Sphaerorhynchus*, Steinina, Stenophora, Stylocephalus, Sycia*, Syncystis, Thalicola*, Thiriotia, Trichotokara, Uradiophora*, Urospora, Xiphocephalus, Zygosoma*, and more.
      • Neogregarinorida Grassé 1953. Apicystis, Aranciocystis, Caulleryella*, Coelogregarina*, Farinocystis*, Gigaductus*, Lipocystis*, Lipotropha*, Lymphotropha*, Machadoella*, Mattesia, Menzbieria, Ophryocystis, Schizocystis*, Syncystis, Tipulocystis*.
      • Cryptogregarinorida Cavalier-Smith 2014, emend. Adl et al. 2019. Cryptosporidium.
    • Blastogregarinea Chatton and Villeneuve 1936, emend. Simdyanov et al. 2018. Chattonaria, Siedleckia.

• Postciliodesmatophora Gerassimova & Seravin 1976
  • Karyorelictea Corliss 1974
    • Kentrophoridae Jankowski 1980. Kentrophoros.
    • Loxodida Jankowski 1980
      • Cryptopharyngidae Jankowski 1980. Cryptopharynx.
      • Loxodidae Bütschli 1889. Loxodes.
    • Geleiidae Kahl 1933. Geleia.
  • Heterotrichea Stein 1859
    • Blepharismidae Jankowski in Small & Lynn 1985. Blepharisma
    • Climacostomidae Repak 1972. Climacostomum.
    • Condylostomatidae Kahl in Doflein & Reichenow 1929. Chattonidium, Condylostoma.
    • Fabreidae Shazib et al. 2014. Fabrea.
    • Gruberiidae Shazib et al. 2014. Gruberia.
    • Coliphorina Jankowski 1967
      • Folliculinidae Dons 1914. Folliculina.
      • Maristentoridae Miao et al. 2005. Maristentor.
    • Peritromidae Stein 1867. Peritromus.
    • Spirostomidae Stein 1867. Anigsteinia, Spirostomum.
    • Stentoridae Carus 1863. Stentor.
• Intramacronucleata Lynn 1996. Incertae sedis: Protocruziidae Jankowski 1980 [Protocruziidia de Puytorac et al. 1987] (Protocruzia Faria da Cunha & Pinto 1922).
  • SAL Gentekaki et al. 2014. Incertae sedis: Cariacotrichea Orsi et al. 2011 (Cariacothrix caudata), Mesodiniidae ankowski, 1980 (Mesodinium), Phacodiniidia Small and Lynn 1985 (Phacodinium).
    • Spirotrichea Bütschli 1889
      • Euplotia Jankowski 1979
        • Euplotida Small & Lynn 1985
          • Aspidiscidae Ehrenberg 1830. Aspidisca.
          • Certesiidae Borror & Hill 1995. Certesia.
          • Euplotidae Ehrenberg 1838. Euplotes.
          • Gastrocirrhidae Fauré-Fremiet 1961. Gastrocirrhus.
          • Uronychidae Jankowski 1975. Diophrys, Uronychia.
        • Discocephalida
          • Discocephalidae Jankowski 1979. Discocephalus, Prodiscocephalus, Paradiscocephalus.
          • Pseudoamphisiellidae Song et al. 1997. Leptoamphisiella, Pseudoamphisiella.
      • Perilemmaphora Berger 2008
        • Hypotrichia Stein 1859
          • Stichotrichida Fauré-Fremiet 1961 (P)^[r]
            • Amphisiellidae Jankowski 1979. Amphisiella, Bistichella.
            • Atractosidae Bourland 2015. Atractos.
            • Epiclintidae Wicklow & Borror 1990. Epiclintes.
            • Gonostomatidae Small & Lynn 1985. Cotterillia, Gonostomum.
            • Halteriidae Claparède & Lachmann 1858. Halteria, Meseres.
            • Holostichidae Fauré-Fremiet 1961. Holosticha, Uncinata.
            • Kahliellidae Tuffrau 1979. Deviata, Kahliella.
            • Keronidae Dujardin 1840. Kerona.
            • Oxytrichidae Ehrenberg 1830 (P). Cyrtohymena, Gastrostyla, Oxytricha, Stylonychia.
            • Parabirojimidae Dai & Xu 2011. Parabirojimia, Tunicothrix.
            • Plagiotomidae Bütschli 1887. Plagiotoma.
            • Psammomitridae Jankowski 1979. Psammomitra.
            • Pseudoamphisiellidae Song et al. 1996. Pseudoamphisiella.
            • Psilotrichidae Bütschli 1889. Psilotricha, Urospinula.
            • Schmidingerotrichidae Foissner 2012. Schmidingerothrix.
            • Spirofilidae von Gelei 1929. Spirofilopsis, Strongylidium.
            • Trachelostylidae Small & Lynn 1985. Trachelostyla.
            • Uroleptidae Foissner & Stoeck 2008. Paruroleptus, Uroleptus.
          • Urostylida Jankowski 1979 (P)
            • Bergeriellidae Liu et al. 2010. Bergeriella, Neourostylopsis.
            • Hemicycliostylidae Lyu et al. 2018. Australothrix, Hemicycliostyla.
            • Pseudokeronopsidae Borror & Wicklow, 1983. Apoholosticha, Pseudokeronopsis.
            • Pseudourostylidae Jankowski 1979. Pseudourostyla.
            • Urostylidae Bütschli 1889. Bakuella, Diaxonella, Urostyla.
        • Oligotrichea Bütschli 1887
          • Oligotrichida Bütschli 1887
            • Cyrtostrombidiidae Agatha 2004. Cyrtostrombidium.
            • Pelagostrombidiidae Agatha 2004. Pelagostrombidium.
            • Strombidiidae Fauré-Fremiet 1970. Strombidium (P).
            • Tontoniidae Agatha 2004. Laboea, Tontonia.
          • Choreotrichida Small & Lynn 1985. Incertae sedis: Lynnella Liu et al. 2011 [Lynnellidae Liu et al. 2011; Lynnellida Liu et al. 2015]
            • Strobilidiina Jankowski 1980 (P)
              • Leegaardiellidae Lynn & Montagnes 1988. Leegaardiella.
              • Lohmanniellidae Montagnes & Lynn 1991. Lohmanniella.
              • Strobilidiidae Kahl in Doflein & Reichenow 1929. Strobilidium.
              • Strombidinopsidae Small & Lynn 1985. Strombidinopsis (P).
            • Tintinnina Kofoid & Campbell 1929. Incertae sedis: Helicostomella, Tintinnopsis (P), several other genera.
              • Ascampbelliellidae Corliss 1960. Ascampbelliella
              • Cyttarocylididae Kofoid & Campbell 1929 [probably synonymous with Petalotrichidae]. Cyttarocylis.
              • Dictyocystidae Haeckel 1873. Dictyocysta.
              • Epiplocylididae Kofoid & Campbell 1939. Epiplocylis.
              • Eutintinnidae Bachy et al. 2012. Dartintinnus, Eutintinnus.
              • Favellidae Kofoid & Campbell 1929. Favella.
              • Nolaclusiliidae Sniezek et al. 1991. Nolaclusilis.
              • Petalotrichidae Kofoid & Campbell 1929 [probably synonymous with Cyttarocylididae]. Petalotricha.
              • Ptychocylididae Kofoid & Campbell 1929. Cymatocylis, Ptychocylis.
              • Rhabdonellidae Kofoid & Campbell 1929. Metacylis, Rhabdonella, Schmidingerella.
              • Stenosemellidae Campbell 1954 (P). Stenosemella.
              • Tintinnidae Claparède & Lachmann 1858. Amphorellopsis, Salpingacantha, Salpingella, Tintinnus.
              • Tintinnidiidae Kofoid & Campbell 1929. Tintinnidium.
              • Undellidae Kofoid & Campbell 1929. Undella.
              • Xystonellidae Kofoid & Campbell 1929. Dadayiella, Parafavella, Xystonella.
      • Licnophoridae Bütschli 1887. Licnophora, Prolicnophora.
      • Kiitrichidae Nozawa 1941. Caryotricha, Kiitricha.
    • Lamellicorticata Vd'ačný et al. 2010
      • Armophorea Lynn 2004. Incertae sedis: Mylestomatidae Kahl in Doflein & Reichenow, 1929 (Mylestoma).
        • Metopida Jankowski 1980 (P)
          • Metopidae Kahl 1927 (P). Bothrostoma, Brachonella, Eometopus, Metopus, Parametopidium, Tesnospira.
          • Apometopidae Foissner 2016. Cirranter, Urostomides.
          • Tropidoatractidae Rotterová et al. 2018. Palmarella, Tropidoatractus.
        • Clevelandellida de Puytorac & Grain 1976
          • Clevelandellidae Kidder 1938. Clevelandella.
          • Inferostomatidae Ky 1971. Inferostoma.
          • Neonyctotheridae Affa'a 1987. Neonyctotherus.
          • Nyctotheridae Amaro 1972 (P). Nyctotherus.
          • Sicuophoridae Amaro 1972. Sicuophora.
        • Caenomorphidae Poche 1913. Caenomorpha, Ludio, Sulfonecta.
        • Odontostomatida Sawaya 1940
          • Discomorphellidae Corliss 1960. Discomorphella.
          • Epalxellidae Corliss 1960. Epalxella, Saprodinium.
      • Litostomatea Small & Lynn 1981
        • Rhynchostomatia Jankowski 1980
          • Dileptida Jankowski 1978
            • Dileptidae Jankowski 1980. Apodileptus, Dileptus, Pseudomonilicaryon.
            • Dimacrocaryonidae Jankowski 1978. Dimacrocaryon, Monomacrocaryon, Rimaleptus.
            • Tracheliidae Ehrenberg 1838. Trachelius.
        • Haptoria Corliss 1974 (P). Incertae sedis: Chaenea.
          • Lacrymariidae de Fromentel 1876. Lacrymaria.
          • Haptorida Corliss 1974
            • Enchelyodonidae Foissner et al. 2002. Enchelyodon, Fuscheria.
            • Homalozoonidae Jankowski 1980. Homalozoon.
            • Pleuroplitidae Foissner 1996. Pleuroplites.
          • Didiniidae Poche 1913. Didinium, Monodinium.
          • Pleurostomatida Schewiakoff 1896
            • Amphileptidae Bütschli 1889. Amphileptus.
            • Litonotidae Kent 1882. Litonotus.
            • Kentrophyllidae Wu et al. 2015. Epiphyllum, Kentrophyllum.
          • Spathidiida Foissner & Foissner 1988
            • Acropisthiidae Foissner & Foissner 1988. Acropisthium, Chaenea.
            • Actinobolinidae Kahl 1930. Actinobolina.
            • Apertospathulidae Foissner et al. 2005. Apertospathula.
            • Enchelyidae Ehrenberg 1838. Enchelys.
            • Pseudoholophryidae Berger et al. 1984. Pseudoholophrya.
            • Spathidiidae Kahl in Doflein & Reichenow 1929. Legendrea,^[77] Spathidium.
            • Trachelophyllidae Kent 1882. Trachelophyllum.
          • Helicoprorodontidae Small & Lynn 1985
        • Trichostomatia Bütschli 1889
          • Vestibuliferida de Puytorac et al. 1974
            • Balantidiidae Reichenow in Doflein and Reichenow 1929. Balantidium, Neobalantidium (P).
            • Buetschliidae Poche 1913. Buetschlia.
            • Paraisotrichidae da Cunha 1917. Paraisotrichia.
            • Protocaviellidae Grain in Corliss 1979. Protocaviella.
            • Protohalliidae da Cunha & Muniz 1927. Protohallia.
            • Pycnotrichidae Poche 1913. Pycnothrix, perhaps Buxtonella.
        • Isoendo
          • Isotrichidae Bütschli 1889. Dasytricha, Isotricha.
          • Entodiniomorphida Reichenow in Doflein & Reichenow 1929
            • Blepharocorythina Wolska 1971
              • Blepharocorythidae Hsiung 1929. Blepharocorys.
              • Parentodiniidae Ito, Miyazaki & Imai 2002. Parentodinium.
              • Pseudoentodiniidae Wolska 1986. Pseudoentodinium.
            • Entodiniomorphina Reichenow in Doflein & Reichenow 1929
              • Cycloposthiidae Poche 1913. Cycloposthium.
              • Gilchristinidae Ito, Ishihara & Imai 2014 [Gilchristidae Ito et al. 2006]. Digilchristia, Gilchristina.^[78]
              • Ophryoscolecidae Stein 1859. Entodinium, Ophryoscolex, Polyplastron.
              • Polydiniellidae Corliss 1960. Polydiniella.
              • Rhinozetidae Van Hoven, Gilchrist & Hamilton-Attwell 1988. Rhinozeta.
              • Spirodiniidae Strelkow 1939. Spirodinium.
              • Telamodiniidae Latteur & Dufey 1967. Telamodinium.
              • Troglodytellidae Corliss 1979. Troglodytella,.
          • Macropodiniida Lynn 2008
            • Amylovoracidae Cameron & O'Donoghue 2002. Amylovorax.
            • Macropodiniidae Dehority 1996. Macropodinium.
            • Polycostidae Cameron & O'Donoghue 2003. Polycosta.
  • CONTHREEP Lynn in Adl et al. 2012 [Ventrata Cavalier-Smith 2004]. Incertae sedis: Askenasia Blochmann 1895, Cyclotrichiidae Jankowski 1980 (Cyclotrichium), Paraspathidium Noland 1937, Pseudotrachelocercidae Song 1990 (Pseudotrachelocerca), Discotrichidae Jankowski 1967 [Discotrichida Fan et al. 2014] (Discotricha, Lopezoterenia).
    • Phyllopharyngea de Puytorac et al. 1974
      • Synhymeniida de Puytorac et al. in Deroux 1978
        • Nassulopsidae Deroux in Corliss 1979. Nassulopsis.
        • Orthodonellidae Jankowski 1968. Orthodonella, Zosterodasys.
        • Scaphidiodontidae Deroux in Corliss 1979. Chilodontopsis, Scaphidiodon.
        • Synhymeniidae Jankowski in Small & Lynn 1985. Synhymenia.
      • Subkinetalia Gong et al. 2009
        • Cyrtophoria Fauré-Fremiet in Corliss 1956
          • Chlamydodontida Deroux 1976 (P)
            • Chilodonellidae Deroux 1970. Chilodonella.
            • Chitonellidae Small & Lynn 1985. Chitonella.
            • Chlamydodontidae Stein 1859. Chlamydodon.
            • Gastronautidae Deroux 1994. Gastronauta.
            • Kryoprorodontidae Alekperov & Mamajeva 1992. Gymnozoum.
            • Lynchellidae Jankowski 1968. Chlamydonella, Lynchella.
          • Dysteriida Deroux 1976
            • Dysteriidae Claparède & Lachmann 1858. Dysteria (P), Trochilia.
            • Hartmannulidae Poche 1913 (P). Hartmannula.
            • Kyaroikeidae Sniezek & Coats 1996. Kyaroikeus.
            • Plesiotrichopidae Deroux 1976. Plesiotrichopus.
            • Chonotrichia Wallengren 1895
              • Exogemmida Jankowski 1972
                • Chilodochonidae Wallengren 1895. Chilodochona.
                • Filichonidae Jankowski 1973. Filichona.
                • Helichonidae Jankowski 1972. Heliochona.
                • Lobochonidae Jankowski 1967. Lobochona.
                • Phyllochonidae Jankowski 1972. Phyllochona.
                • Spirochonidae Stein 1854. Spirochona.
              • Cryptogemmida Jankowski 1975
                • Actinichonidae Jankowski 1973. Actinichona.
                • Echinichonidae Jankowski 1973. Echinichona.
                • Inversochonidae Jankowski 1973. Inversochona.
                • Isochonidae Jankowski 1973. Isochona.
                • Isochonopsidae Batisse & Crumeyrolle 1988. Isochonopsis.
                • Stylochonidae Mohr 1948. Stylochona.
        • Rhynchodia Chatton & Lwoff 1939
          • Hypocomidae Bütschli 1889. Hypocoma.
          • Rhynchodida Chatton & Lwoff 1939
            • Ancistrocomidae Chatton & Lwoff 1939. Ancistrocoma.
            • Sphenophryidae Chatton & Lwoff 1921. Sphenophrya.
        • Suctoria Claparède & Lachmann 1858
          • Exogenida Collin 1912
            • Allantosomatidae Jankowski 1967. Allantosoma.
            • Dentacinetidae Batisse 1992. Dentacineta.
            • Dendrosomididae Jankowski 1978. Dendrosomides.
            • Ephelotidae Kent 1882. Ephelota.
            • Lecanophryidae Jankowski 1973. Lecanophrya.
            • Manuelophryidae Dovgal 2002. Manuelophrya.
            • Metacinetidae Bütschli 1889. Metacineta.
            • Ophryodendridae Stein 1867. Ophryodendron.
            • Paracinetidae Jankowski 1978. Paracineta.
            • Phalacrocleptidae Kozloff 1966. Phalacrocleptes.
            • Podophryidae Haeckel 1866. Podophrya.
            • Praethecacinetidae Dovgal 1996. Praethecacineta.
            • Rhabdophryidae Jankowski 1970. Rhabdophrya.
            • Severonidae Jankowski 1981. Severonis.
            • Spelaeophryidae Jankowski in Batisse 1975. Spelaeophrya.
            • Tachyblastonidae Grell 1950. Tachyblaston.
            • Thecacinetidae Matthes 1956. Thecacineta.
          • Endogenida Collin 1912
            • Acinetidae Stein 1859. Acineta.
            • Acinetopsidae Jankowski 1978. Acinetopsis.
            • Choanophryidae Dovgal 2002. Choanophrya.
            • Corynophryidae Jankowski 1981. Corynophrya.
            • Dactylostomatidae Jankowski 1978. Dactylostoma.
            • Dendrosomatidae Fraipont 1878. Dendrosoma.
            • Endosphaeridae Jankowski in Corliss 1979. Endosphaera.
            • Erastophryidae Jankowski 1978. Erastophrya.
            • Pseudogemmidae Jankowski 1978. Pseudogemma.
            • Rhynchetidae Jankowski 1978. Rhyncheta.
            • Solenophryidae Jankowski 1981. Solenophrya.
            • Tokophryidae Jankowski in Small & Lynn 1985. Tokophrya.
            • Trichophryidae Fraipont 1878. Trichophrya.
          • Evaginogenida Jankowski in Corliss 1979
            • Cometodendridae Jankowski 1978. Cometodendron.
            • Cyathodiniidae da Cuhna 1914. Cyathodinium.
            • Dendrocometidae Haeckel 1866. Dendrocometes.
            • Discophryidae Collin 1912. Discophrya.
            • Enchelyomorphidae Augustin & Foissner 1992. Enchelyomorpha.
            • Heliophryidae Corliss 1979. Heliophrya.
            • Periacinetidae Jankowski 1978. Periacineta.
            • Prodiscophryidae Jankowski 1978. Prodiscophrya.
            • Rhynchophryidae Jankowski 1978. Rhynchophrya.
            • Stylocometidae Jankowski 1978. Stylocometes.
            • Trypanococcidae Dovgal 2002. Trypanococcus.
    • Colpodea Small & Lynn 1981
      • Bursariomorphida Fernández-Galiano 1978
        • Bryometopidae Jankowski 1980. Bryometopus (P), Thylakidium.
        • Bursaridiidae Foissner 1993. Bursaridium, Paracondylostoma.
        • Bursariidae Bory de St. Vincent 1826. Bursaria.
      • Colpodida de Puytorac et al. 1974. Incertae sedis: Bardeliellidae Foissner 1984 (Bardeliella), Hausmanniellidae Foissner 1987 (Avestina, Hausmanniella), Ilsiellidae Bourland et al. 2011 (Ilsiella), Pseudochlamydonellidae Buitkamp et al. 1989 (Hackenbergia, Pseudochlamydonella) and Marynidae Poche 1913 (Maryna).
        • Bryophryina de Puytorac et al. 1979
          • Bryophryidae de Puytorac et al. 1979. Bryophrya.
          • Sandmanniellidae Foissner & Stoeck 2009. Sandmanniella.
        • Colpodina Foissner et al. 2011
          • Colpodidae Bory de St. Vincent 1826 (P). Colpoda.
          • Grandoriidae Corliss 1960. Grandoria.
          • Tillinidae Foissner et al. 2011. Tillina.
        • Grossglockneriidae Foissner 1980 [Grossglockneriina Foissner 1980]. Grossglockneria, Pseudoplatyophrya.
      • Cyrtolophosidida Foissner 1978
        • Cyrtolophosididae Stokes 1888. Cyrtolophosis.
        • Kreyellidae Foissner 1979. Kreyella.
      • Platyophryida de Puytorac et al. 1979
        • Ottowphryidae Foissner et al. 2011. Ottowphrya, Platyophryides.
        • Platyophryidae de Puytorac et al. 1979 (P). Platyophrya.
        • Sagittariidae Grandori & Grandori 1935. Sagittaria.
        • Sorogenidae Bradbury & Olive 1980. Sorogena.
        • Woodruffiidae Gelei 1954. Etoschophrya, Rostrophrya, Woodruffia.
    • Nassophorea (P)
      • Colpodidiidae Foissner 1995. Colpodidium.
      • Nassulida Jankowski 1967
        • Furgasoniidae Corliss 1979. Furgasonia, Wolfkosia.
        • Nassulidae de Fromentel 1874. Nassula, Obertrumia.
      • Microthoracida Jankowski 1967
        • Microthoracidae Wrzesniowski 1870. Drepanomonas, Microthorax.
        • Leptopharyngidae Kahl 1926. Leptopharynx, Pseudomicrothorax.
    • Prostomatea Schewiakoff 1896 (P)
      • Apsiktratidae Foissner et al. 1994 [Prostomatida Schewiakoff 1896]
        • Balanionidae Small & Lynn 1985. Balanion.
        • Cryptocaryonidae Wright & Colorni 2002. Cryptocaryon.
        • Colepidae Ehrenberg 1838. Coleps, Plagiopogon.
        • Holophryidae Perty 1852. Holophrya.
        • Lagynidae Sola et al. 1990. Lagynus.
        • Metacystidae Kahl 1926. Metacystis, Vasicola.
        • Placidae Small & Lynn 1985. Placus.
        • Plagiocampidae Kahl 1926. Plagiocampa.
        • Prorodontidae Kent 1881. Prorodon.
        • Urotrichidae Small & Lynn 1985. Urotricha.
    • Plagiopylea Small & Lynn 1985
      • Plagiopylida Small & Lynn 1985
        • Epalxellidae Corliss 1960. Epalxella, Saprodinium.
        • Plagiopylidae Schewiakoff 1896. Plagiopyla.
        • Sonderiidae Small & Lynn 1985. Sonderia.
        • Trimyemidae Kahl 1933. Trimyema.
    • Oligohymenophorea de Puytorac et al. 1974
      • Apostomatia Chatton & Lwoff 1928
        • Apostomatida Chatton & Lwoff 1928
          • Colliniidae Cépède 1910. Collinia, Metacollinia.
          • Cyrtocaryidae Corliss 1979. Cyrtocaryum.
          • Foettingeriidae Chatton 1911. Foettingeria.
          • Pseudocolliniidae Chantangsi et al. 2013. Fusiforma, Pseudocollinia.
        • Astomatophorida Jankowski 1966
          • Opalinopsidae Hartog 1906. Opalinopsis.
        • Pilisuctorida Jankowski 1966
          • Conidophryidae Kirby 1941. Conidophrys.
      • Astomatia Schewiakoff 1896
        • Anoplophryidae Cépède 1910. Anoplophrya.
        • Buetschliellidae de Puytorac in Corliss 1979. Buetschliella.
        • Clausilocolidae de Puytorac in Corliss 1979. Clausilocola.
        • Contophryidae de Puytorac 1972. Contophyra.
        • Haptophryidae Cépède 1923. Haptophrya.
        • Hoplitophryidae Cheissin 1930. Hoplitophrya.
        • Intoshellinidae Cépède 1910. Intoshellina.
        • Maupasellidae Cépède 1910. Maupasella.
        • Radiophryidae de Puytorac 1972. Radiophrya.
      • Hymenostomatia Delage & Hérouard 1896
        • Tetrahymenida Fauré-Fremiet in Corliss 1956. Incertae sedis: Trichospiridae Kahl 1926 (Trichospira).
          • Curimostomatidae Jankowski 1968. Curimostoma.
          • Glaucomidae Corliss 1971. Glaucoma.
          • Spirozonidae Kahl 1926. Spirozona.
          • Tetrahymenidae Corliss 1952. Tetrahymena.
          • Turaniellidae Didier 1971. Colpidium, Dexiostoma, Turaniella.
        • Ophryoglenida Canella 1964
          • Ichthyophthiriidae Kent 1881. Ichthyophthirius.
          • Ophryoglenidae Kent 1881. Ophryoglena.
      • Peniculia Fauré-Fremiet in Corliss 1956 (P)
        • Peniculida Fauré-Fremiet in Corliss 1956
          • Clathrostomatidae Kahl 1926. Clathrostoma.
          • Frontoniidae Kahl 1926. Disematostoma, Frontonia (P).
          • Lembadionidae Jankowski in Corliss 1979. Lembadion.
          • Maritujidae Jankowski in Small & Lynn 1985. Marituja.
          • Neobursaridiidae Dragesco & Tuffrau 1967. Neobursaridium.
          • Parameciidae Dujardin 1840. Paramecium.
          • Paranassulidae Fauré-Fremiet 1962. Paranassula.
          • Stokesiidae Roque 1961. Stokesia.
        • Urocentridae Claparède & Lachmann 1858 [Urocentrida de Puytorac, Grain & Mignot 1987]
      • Peritrichia Stein 1859
        • Sessilida Kahl 1933
          • Astylozoidae Kahl 1935. Astylozoon, Hastatella.
          • Ellobiophryidae Chatton and Lwoff 1929. Ellobiophrya.
          • Epistylididae Kahl 1933. Epistylis.
          • Lagenophryidae Bütschli 1889. Lagenophrys.
          • Operculariidae Fauré-Fremiet in Corliss 1979. Opercularia.
          • Rovinjellidae Matthes 1972. Rovinjella.
          • Scyphidiidae Kahl 1933 (P). Scyphidia.
          • Termitophryidae Lom in Corliss 1979. Termitophrya.
          • Usconophryidae Clamp 1991. Usconophrys.
          • Vaginicolidae de Fromentel 1874. Cothurnia, Pyxicola, Thuricola, Vaginicola.
          • Vorticellidae Ehrenberg 1838. Carchesium, Epicarchesium (P), Ophrydium, Pelagovorticella, Pseudovorticella (P), Vorticella (P).
          • Zoothamniidae Sommer 1951. Haplocaulus, Zoothamnium.
        • Mobilida Kahl 1933
          • Polycyclidae Poljansky 1951. Polycycla.
          • Trichodinidae Claus 1874. Trichodina.
          • Trichodinopsidae Kent 1881. Trichodinopsis.
          • Urceolariidae Dujardin 1840. Leiotrocha, Urceolaria.
      • Scuticociliatia Small 1967 (P)
        • Philasterida Small 1967
          • Cohnilembidae Kahl 1933. Cohnilembus.
          • Cryptochilidae Berger in Corliss 1979. Cryptochilum.
          • Entodiscidae Jankowski 1973. Entodiscus.
          • Entorhipidiidae Madsen 1931. Entorhipidium.
          • Orchitophryidae Cépède 1910 (P). Orchitophrya.
          • Paralembidae Corliss & de Puytorac in Small & Lynn 1985. Anophrys, Paralembus.
          • Parauronematidae Small & Lynn 1985 (P). Parauronema (P).
          • Philasteridae Kahl 1931. Kahlilembus, Philaster.
          • Pseudocohnilembidae Evans & Thompson 1964. Pseudocohnilembus.
          • Schizocaryidae Jankowski 1979. Schizocaryum.
          • Thigmophryidae Chatton & Lwoff 1926. Thigmophrya.
          • Thyrophylacidae Berger in Corliss 1961. Thyrophylax.
          • Uronematidae Thompson 1964. Uronema.
          • Urozonidae Grolière 1975. Urozona.
        • Pleuronematida Fauré-Fremiet in Corliss 1956
          • Calyptotrichidae Small & Lynn 1985. Calyptotricha.
          • Conchophthiridae Kahl in Doflein and Reichenow 1929. Conchophthirus.
          • Ctedoctematidae Small & Lynn 1985. Ctedoctema.
          • Cyclidiidae Ehrenberg 1838 (P). Cristigera, Cyclidium.
          • Dragescoidae Jankowski 1980. Dragescoa.
          • Eurystomatellidae Miao et al. 2010. Eurystomatella.
          • Histiobalantiidae de Puytorac & Corliss in Corliss 1979. Histiobalantium.
          • Peniculistomatidae Fenchel 1965. Peniculistoma.
          • Pleuronematidae Kent 1881 (P). Pleuronema.
          • Thigmocomidae Kazubski 1958. Thigmocoma.
        • Thigmotrichida Chatton & Lwoff 1922
          • Ancistridae Issel 1903. Ancistrum.
          • Hemispeiridae König 1894. Hemispeira.
          • Hysterocinetidae Diesing 1866. Hysterocineta.
          • Paraptychostomidae Ngassam et al. 1994. Paraptychostomum.
        • Loxocephalida Jankowski 1964 (P)
          • Cinetochilidae Perty 1852 (P). Cinetochilum, Sathrophilus.
          • Loxocephalidae Jankowski 1964. Cardiostomatella, Dexiotricha, Loxocephalus.