变形虫门（Amoebozoa）
*Tubulinea
**Arcellinida
**Leptomyxida
**Tubulinida
**目未定及环境样本
*Pelobiontea
**Pelobiontida
*Entamoebea
**Entamoebida
*Flabellinea
**Dactylopodida
**Dermamoebida
**Himatismenida
**Vannellida
*Myxomycetes
**Echinosteliales
**Liceales
**Physarales
**Trichiales
**Stemonitales
**目未定
*Dictyosteliomycetes
**Dictyosteliales
*Protosteliomycetes
**Protosteliales
*纲未定及环境样本
顶复门（Apicomplexa）
*Aconoidasida
**Haemosporida
**Piroplasmorida
*Conoidasida
**Archigregarinorida
**Eugregarinorida
**Neogregarinorida
**目未定及环境样本
*Coccidiasina
**Agamococcidiorida
**Eucoccidiorida
**Ixorheorida
**Protococcidiorida
**目未定及环境样本
*纲未定及环境样本
无根虫门（Apusozoa）
*Diphyllatea
**Diphylleida
*Thecomonadea
**Ancyromonadida
**Apusomonadida
**Hemimastigida
*纲未定及环境样本
丝足虫门（Cercozoa）
*Ascetosporea
**Claustrosporida
**Haplosporida
**Paramyxida
*Gromiidea
**Gromiida
*Phytomyxea
**Phagomyxida
**Plasmodiophorida
**目未定
*Imbricatea
**Euglyphida
**Thaumatomonadida
*Sarcomonadea
**Cercomonadida
**Metopiida
**目未定
*Thecofilosea
**Cryomonadida
**Tectofilosida
*Chlorarachnea
**Chlorarachniida
*Proteomyxidea
**Heliomonadida
**Leucodictyida
**Pseudosporida
**Reticulosida
*Spongomonadea
**Spongomonadida
*纲未定及环境样本
轮藻门（Charophyta）
*Mesostigmatophyceae
**Mesostigmales
**环境样本
*Klebsormidiophyceae
**Klebsormidiales
*Zygnematophyceae
**Zygnematales
**Desmidiales
*Charophyceae
**Charales
*Coleochaetophyceae
**Coleochaetales
*纲未定及环境样本
绿藻门（Chlorophyta）
*Chlorophyceae
**Chaetopeltidales
**Chaetophorales
**Chlorococcales
**Chlorocystidales
**Microsporales
**Oedogoniales
**Sphaeropleales
**Tetrasporales
**Volvocales
**目未定及环境样本
*Mamiellophyceae
**Mamiellales
**目未定
*Nephroselmidophyceae
**Nephroselmiales
*Pedinophyceae
**Pedinomonadales
**Scourfieldiales
**目未定
*Pleurastrophyceae
**Chlorodendrales
**Prasinococcales
**Pseudoscourfieldiales
**Pyramimonadales
**目未定及环境样本
*Trebouxiophyceae
**Chlorellales
**Oocystales
**Prasiolales
**Trebouxiales
**目未定及环境样本
*Ulvophyceae
**Acrosiphoniales
**Bryopsidales
**Chlorocystidales
**Cladophorales
**Dasycladales
**Ignatiales
**Oltmansiellopsidales
**Scotinosphaerales
**Trentepohliales
**Ulotrichales
**Ulvales
**目未定及环境样本
*纲未定及环境样本
领鞭毛虫门（Choanozoa）
*Aphelidea
*Choanoflagellata
**Choanoflagellida
*Corallochytrea
**Corallochytrida
*Cristidiscoidea
**Ministeriida
**Nucleariida
*Mesomycetozoea
**Amoebidiales
**Dermocystida
**Eccrinales
**Ichthyophonida
**目未定
*纲未定
Chromerida
*Chromeraceae
**Chromera
*Vitrellaceae
**Vitrella
*纲未定
纤毛虫门（Ciliophora）
*Colpodea
**Bryometopida
**Bryophryida
**Bursariomorphida
**Colpodida
**Cyrtolophosidida
**Sorogenida
**目未定及环境样本
*Litostomatea
**Cyclotrichida
**Haptorida
**Pleurostomatida
**Entodiniomorphida
**Trichostomatida
**Vestibuliferida
**目未定及环境样本
*Nassophorea
**Microthoracida
**Nassulida
**Synhymeniida
**目未定
*Oligohymenophorea
**Apostomatida
**Astomatophorida
**Pilisuctorida
**Astomatida
**Hymenostomatida
**Peniculida
**Mobilida
**Sessilida
**Philasterida
**Pleuronematida
**Thigmotrichida
**目未定及环境样本
*Phyllopharyngea
**Cryptogemmida
**Exogemmida
**Chlamydodontida
**Dysteriida
**Hypocomatida
**Rhynchodida
**Endogenida
**Evaginogenida
**Exogenida
**目未定及环境样本
*Plagiopylea
**Odontostomatida
**Plagyopylida
**环境样本
*Prostomatea
**Prorodontida
**Prostomatida
**环境样本
*Spirotrichea
**Choreotrichida
**Tintinnida
**Euplotida
**Kiitrichida
**Halteriida
**Oligotrichida
**Strombidiida
**Protocruziida
**Plagiotomida
**Sporadotrichida
**Stichotrichida
**Urostylida
**Armophorida
**Clevelandellida
**Odontostomatida
**Phacodiniida
**目未定及环境样本
*Heterotrichea
**Heterotrichida
**Licnophorida
**环境样本
*Karyorelictea
**Loxodida
**Protoheterotrichida
**Protostomatida
**目未定及环境样本
*纲未定及环境样本
隐藻门 (Cryptophyta)
*Cryptomonadea
**Cryptomonadales
**Pyrenomonadales
**Tetragonidiales
*Goniomonadea
**Goniomonadales
*Katablepharidophyceae
**Katablepharidales
*纲未定及环境样本
双鞭毛虫门（Dinoflagellata）
*Blastodiniophyceae
**Blastodiniales
*Dinophyceae
**Dinophysiales
**Gymnodiniales
**Ptychodiscales
**Gonyaulacales
**Peridiniales
**Prorocentrales
**Chytriodiniales
**Desmocapsales
**Dinamoebales
**Dinocloniales
**†Hystrichosphaerida
**Phytodiniales
**Suessiales
**Thoracosphaerales
**Zooxanthellales
**目未定
*Noctiluciphyceae
**Noctilucales
*Syndiniophyceae
**Syndiniales
*Apicomonadea
**Colpodellida
**目未定及环境样本
*Colponemea
**Colponemida
*Ellobiopsea
**Ellobiopsida
*Perkinsea
**Perkinsorida
**目未定
*†Acritarcha
**†Acanthomorphitae
**†Diacromorphitae
**†Dinetromorphitae
**†Disphaeromorphitae
**†Herkomorphitae
**†Netromorphitae
**†Oomorphitae
**†Platymorphitae
**†Polygonomorphitae
**†Prismatomorphitae
**†Pteromorphitae
**†Sphaeromorphitae
**†Stephanomorphitae
**†Versimorphitae
**目未定
*纲未定及环境样本
眼虫门（Euglenozoa）
*Diplonemea
**Diplonemida
*Euglenoidea
**Euglenida
**Peranemida
**Petalomonadida
**Rhabdomonadida
**目未定
*Kinetoplastea
**Bodonida
**Trypanosomatida
*Postgaardea
**Postgaardida
*纲未定及环境样本
有孔虫门（Foraminifera）
*Allogromioidia
**Allogromiida
*Athalamea
**Biomyxida
*†Fusulinidia
**†Fusulinida
*Miliolidia
**Miliolida
*Rotalidia
**Carterinida
**Globigerinida
**†Involutinida
**Lagenida
**Robertinida
**Rotaliida
**Silicoloculinida
**Spirillinida
*Textularidia
**Astrorhizida
**Textulariida
*Xenophyophorea
**†Paleodictyida
**Psamminida
**Stannomida
*纲未定及环境样本
灰胞藻门（Glaucophyta）
*Glaucophyceae
**Cyanophorales
**Glaucocystales
**Gloeochaetales
**目未定及环境样本
槽虫门（Loukozoa）
*Jakobea
**Jakobida
*Malawimonadea
**Malawimonadida
后滴门（Metamonada）
*Carpediemonadea
**Carpediemonadida
*Anaeromonadida
**Trimastigida
**Oxymonadida
*Retortamonadea
**Retortamonadida
*Trepomonadea
**Enteromonadida
**Distomatida
**Giardiida
*Trichomonadea
**Lophomonadida
**Spirotrichonymphida
**Trichomonadida
*Trichonymphea
**Trichonymphida
*纲未定及环境样本
定鞭藻门 (Haptophyta)
*Prymnesiophyceae
**Coccolithales
**Coccosphaerales
**Isochrysidales
**Phaeocystales
**Prymnesiales
**Syracosphaerales
**Zygodiscales
**†Arkhangelskiales
**†Discoasterales
**†Eiffelithales
**†Podorhabdales
**†Stephanolithiales
**†Watznaueriales
*Pavlovophyceae
**Pavlovales
*纲未定及环境样本
不等鞭毛门 (Heterokontophyta)
*Hyphochytriomycetes
**Hyphochytriales
*Labyrinthulomycetes
**Labyrinthulales
**Thraustochytriales
**目未定及环境样本
*Opalinea
**Slopalinida
*Bicosecophyceae
**Bicosoecales
**Pirsoniales
*Peronosporomycetes
**Albuginales
**Olpidiopsidales
**Peronosporales
**Pythiales
**Rhipidiales
**Leptomitales
**Salilagenidiales
**Saprolegniales
**Sclerosporales
**Anisolpidiales
**†Galtierella
**Lagenidiales
**Lagenismatales
**Myzocytiopsidales
**Rozellopsidales
**目未定及环境样本
*Chrysophyceae
**Chromulinales
**Chrysamoebidales
**Chrysapiales
**Chrysocapsales
**Chrysosphaerales
**Hibberdiales
**Hydrurales
**Ochromonadales
**Phaeothamniales
**Rhizochrysidales
**Thallochrysidales
**目未定及环境样本
*Eustigmatophyceae
**Eustigmatales
**目未定及环境样本
*Phaeothamniophyceae
**Phaeothamniales
**Pleurochloridellales
**目未定及环境样本
*Raphidophyceae
**Raphidomonadales
**目未定及环境样本
*Synurophyceae
**Synurales
**目未定及环境样本
*Phaeophyceae
**Ascoseirales
**Chordariales
**Cutleriales
**Desmarestiales
**Dictyosiphonales
**Dictyotales
**Durvillaeales
**Ectocarpales
**Fucales
**Laminariales
**Scytosiphonales
**Scytothamnales
**Sphacelariales
**Sporochnales
**Tilopteridales
**目未定
*Xanthophyceae
**Chloramoebales
**Heterogloeales
**Mischococcales
**Rhizochloridales
**Tribonematales
**Vaucheriales
**目未定及环境样本
*Chrysomerophyceae
**Chrysomeridales
*Actinochrysophyceae
**Actinophryida
**Ciliophryida
**Pedinellales
**Rhizochromulinales
**Dictyochales
**目未定及环境样本
*Pelagophyceae
**Pelagomonadales
**Sarcinochrysidales
**目未定及环境样本
*Bolidophyceae
**Bolidomonadales
*Coscinodiscophyceae
**Thalassiosirales
**Chrysanthemodiscales
**Melosirales
**Paraliales
**Aulacoseirales
**Orthoseirales
**Coscinodiscales
**Ethmodiscales
**Asterolamprales
**Arachnoidiscales
**Stictodiscales
**Stictocyclales
**Triceratiales
**Biddulphiales
**Hemiaulales
**Anaulales
**Lithodesmiales
**Corethrales
**Cymatosirales
**Rhizosoleniales
**Leptocylindrales
**Chaetocerotales
**目未定及环境样本
*Fragilariophyceae
**Fragilariales
**Tabellariales
**Licmophorales
**Rhaphoneidales
**Ardissoneales
**Toxariales
**Thalassionematales
**Rhabdonematales
**Striatellales
**Cyclophorales
**Climacospheniales
**Protoraphidales
**目未定及环境样本
*Bacillariophyceae
**Eunotiales
**Lyrellales
**Mastogloiales
**Dictyoneidales
**Cymbellales
**Achnanthales
**Naviculales
**Thalassiophysales
**Bacillariales
**Rhopalodiales
**Surirellales
**目未定及环境样本
*Xanthomonadophyceae
*Blastocystae
**Blastocystida
*纲未定及环境样本
透色门（Percolozoa）
*Heterolobosea
**Acrasida
**Lyromonadida
**Schizopyrenida
**目未定及环境样本
*Percolatea
**Percolomonadida
**Pseudociliatida
放射虫门（Radiolaria）
*Acantharea
**Arthracanthida
**Chaunacanthida
**Holacanthida
**Symphyacanthida
**目未定及环境样本
*Phaeodarea
**Phaeocalpida
**Phaeoconchida
**Phaeocystida
**Phaeodendrida
**Phaeogromida
**Phaeogymnocellida
**Phaeosphaerida
*Polycystina
**†Albaillellaria
**Archaeospicularia
**Collodaria
**Entactinaria
**†Latentifistularia
**Nassellaria
**Spumellaria
**目未定及环境样本
*Sticholonchea
**Taxopodida
**环境样本
*纲未定及环境样本
红藻门（Rhodophyta）
*Rhodophyceae
**Bangiales
**Goniotrichales
**Porphyridiales
**Ahnfeltiales
**Pihiellales
**Corallinales
**Rhodogorgonales
**Hildenbrandiales
**Acrochaetiales
**Balbianiales
**Balliales
**Batrachospermales
**Colaconematales
**Nemaliales
**Palmariales
**Bonnemaisoniales
**Ceramiales
**Gelidiales
**Gigartinales
**Gracilariales
**Halymeniales
**Nemastomatales
**Plocamiales
**Rhodymeniales
**目未定及环境样本
*Cyanidiophyceae
*纲未定及环境样本
门未定
*其余的原生生物种类（包括早期原生生物种类及混合生物片段、X细胞寄生物）
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