| Acavomonidia | | Acavomonadea | Acavomonadida (Acavomonas) |
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| Ciliophora | | Intramacronucleata | - Armophorea (Metopus)
- Cariacotrichea (Cariacothrix caudata)
- Colpodea (Colpoda)
- Litostomatea (Balantidium, Dileptus)
- Muranotrichea (Muranothrix)
- Nassophorea (Nassula)
- Oligohymenophorea (Ichthyophthirius, Paramecium, Tetrahymena, Vorticella)
- Parablepharismea (Parablepharisma)
- Phyllopharyngea (Chilodonella, Tokophrya)
- Plagiopylea (Plagiopyla)
- Prostomatea (Coleps, Holophrya)
- Protocruziea (Protocruzia)
- Spirotrichea (Euplotes, Stylonychia)
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| Postciliodesmatophora | - Heterotrichea (Stentor, Climacostomum, Blepharisma)
- Karyorelictea (Loxodes, Tracheloraphis)
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Mesodiniea (Mesodinium, Myrionecta) |
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| Colponemidia | | Colponemadea | Colponemadida (Colponema) |
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Myzozoa | | | Aconoidasida | | Haemospororida | - Garniidae (Garnia)
- Haemoproteidae (Haemoproteus)
- Leucocytozoidae (Leucocytozoon)
- Plasmodiidae (Plasmodium)
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| Piroplasmida | - Babesiidae (Babesia)
- Theileriidae (Theileria)
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- Cardiosporidium
- Nephromyces
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| Conoidasida | | | Agamococcidiorida | - Gemmocystidae (Gemmocystis)
- Rhytidocystidae (Rhytidocystis)
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| Eucoccidiorida | | Adeleorina | - Adeleidae
- Dactylosomatidae (Babesiosoma, Dactylosoma)
- Haemogregarinidae (Haemogregarina)
- Hepatozoidae (Hepatozoon)
- Karyolysidae (Karyolysus)
- Klossiellidae (Klossiella)
- Legerellidae (Legerella)
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| Eimeriorina | - Aggregatidae (Aggregata, Grasseella, Merocystis, Ovivora, Pseudoklossia, Selysina)
- Atoxoplasmatidae
- Barrouxiidae
- Calyptosporiidae
- Caryotrophidae
- Cryptosporidiidae (Cryptosporidium)
- Eimeriidae (Cyclospora, Eimeria, Isospora)
- Elleipsisomatidae
- Lankesterellidae
- Selenococcidiidae
| | Sarcocystidae | - Sarcocystinae (Frenkelia, Sarcocystis)
- Toxoplasmatinae (Besnoitia, Hammondia, Hyaloklossia, Nephroisospora, Neospora, Toxoplasma)
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| Ixorheorida | |
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| Protococcidiorida | - Angeiocystidae (Angeiocystis)
- Eleutheroschizonidae (Coelotropha, Defretinella, Eleutheroschizon)
- Grelliidae (Coelotropha, Grellia)
- Mackinnoniidae (Mackinnonia)
- Myriosporidae (Myriosporides, Myriospora)
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Gregarinia | | Archigregarinorida | - Exoschizonidae (Exoschizon)
- Selenidioididae (Merogregarina, Meroselenidium, Selenidioides, Veloxidium)
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| Eugregarinorida | | Aseptatorina | - Aikinetocystidae
- Allantocystidae
- Diplocystidae
- Enterocystidae
- Ganymedidae
- Lecudinidae
- Monocystidae (Monocystinae, Oligochaetocystinae, Rhynchocystinae, Stomatophorinae, Zygocystinae)
- Schaudinnellidae
- Selenidiidae
- Thiriotiidae
- Urosporidae
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| Blastogregarinorina | - Siedleckiidae (Siedleckia)
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| Septatorina | - Fusionicae (Fusionidae)
- Gregarinicae (Cephaloidophoridae, Cephalolobidae, Didymophoridae, Gregarinidae, Hirmocystidae, Metameridae, Uradiophoridae)
- Porosporicae (Porosporidae)
- Stenophoricae (Acutidae, Amphiplatysporidae, Brustiophoridae, Cnemidosporidae, Dactylophoridae, Leidyanidae, Monoductidae, Monoicidae, Sphaerocystidae, Stenophoridae, Trichorhynchidae)
- Stylocephaloidea (Actinocephalidae, Stylocephalidae)
- Blabericolidae
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| Neogregarinorida | - Schizogregarinina (Caulleryellidae, Ophryocystidae)
- Gigaductidae (Gigaductus)
- Lipotrophidae (Apicystis, Farinocystis, Lipotropha, Lipocystis, Mattesia, Menzbieria)
- Schizocystidae (Lymphotropha, Machadoella, Schizocystis)
- Syncystidae (Syncystis)
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| Apicomonadea | | Chromerida | - Chromeraceae (Chromera velia)
- Vitrellaceae (Vitrella brassicaformis)
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| Colpodellida | - Colpodellidae (Colpodella)
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| Voromonadida | - Alphamonadidae (Alphamonas)
- Voromonadidae (Voromonas)
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| Dinoflagellata | | Dinokaryota | |
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| Noctilucea | |
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| Syndinea | - Syndiniales: Amoebophryaceae (Amoebophyra)
- Duboscquellaceae (Duboscquella)
- Syndiniaceae (Hematodinium, Syndinium)
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| Diğer | - Acrocoelidae (Acrocoelus)
- Ichthyodinium
- Oxyrrhinaceae (Oxyrrhis)
- Pronoctilucidae (Pronoctiluca)
- Psammosidae (Psammosa)
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| Perkinsozoa | | Perkinsea | - Perkinsidae (Perkinsus)
- Phagodinida (Phagodinium)
- Rastromonadida (Parvilucifera, Rastrimonas)
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| Protoalveolata | | Ellobiopsea | - Ellobiopsidae (Elliobiocystis, Ellobiopsis, Parallobiopsis, Thalassomyces, Rhizellobiopsis)
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| Myzomonadea | |
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| Squirmidea | - Squirmidae (Filipodium, Platyproteum)
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