[ref. ID; 1663 (Robert W. Pennak, 1978)]
Class Phytomastigophorea
Order Dinoflagellida
- Family Cystodiniidae
Genus: Glenodinium
- Family Gymnodiniidae
Genus: Amphidinium, Hemidinium, Gymnodinium, Gyrodinium
- Family Peridiniidae
Genus: Ceratium, Gonyoaulax, Peridinium
- Family Phytodiniidae
Genus: Phytodinium
Order Chrysomonadida
Suborder Euchrysomonadina
- Family Chromuinidae
Genus: Chromulina, Chrysamoeba, Chrysapsis, Chrysococcus, Chrysosphaerella, Chrysopyxis, Kephyrion, Mallomonas
- Family Syncryptidae
Genus: Derepyxis, Hymenomonas, Snycrypta, Synura
- Family Ochromonadidae
Genus: Cyclonexis, Dinobryon, Hyalobryon, Ochromonas, Uroglena, Uroglenopsis
Suborder Rhizochrysidina
Genus: Rhizochrysis
Suborder Chrysocapsina
Genus: Hydrurus
Order Cryptomonadida
- Family Cryptomonadidae
Genus: Chilomonas, Cryptochrysis, Cryptomonas, Cyathomonas, Rhodomonas
- Family Nephroselmidae
Genus: Nephroselmis
Order Volvocida
- Family Volvocidae
Genus: Chlamydobotrys, Eudorina, Gonium, Pandorina, Platydorina, Pleodorina, Spondylomorum, Volvox
- Family Phacotidae
Genus: Phacotus, Pteromonas
- Family Chlamydomonadidae
Genus: Chlamydomonas, Chlorogonium, Haematococcus, Lobomonas, Coccomonas, Gloeomonas, Hyalogonium, Parapolytoma, Polytoma, Thorakomonas
- Family Trichlorididae
Genus: Trichloris
- Family Carteriidae
Genus: Carteria, Polytomella, Pyramimonas, Spermatozopsis
- Family Chlorasteridae
Genus: Chloraster
- Family Polyblepharididae
Genus: Pocillomonas
Order Chloromonadida
Genus: Gonyostomum, Thaumatomastix, Trentonia, Vacuolaria
Order Euglenida
- Family Euglenidae
Genus: Ascoglena, Colacium, Cryptoglena, Euglena, Khawkinea, Lepocinclis, Phacus, Trachelomonas
- Family Astasiidae
Genus: Astasia, Menoidium, Peranema, Petalomonas, Scytomonas, Urceolus
- Family Anisonemidae
Genus: Anisonema, Distigma, Entosiphon, Heteronema, Notosolenus
Class Mastigophorea
- Family Amphimonadidae
Genus: Amphimonas, Cladomonas, Dinomonas, Diplomita, Rhipidodendron, Spiromonas, Spongomonas
- Family Phalansteriidae
Genus: Phalansterium
Class Zoomastigophorea
Order Rhizomastigida
Suborder Euchrysomonadina
- Family Chromulinidae
Genus: Oikomonas
- Family Phalansteriidae
Genus: Phalansterium
- Family Codosigidae
Genus: Codosiga, Desmarella, Diplosiga, Monosiga, Protospongia, Sphaeroeca
- Family Bicosoecidae
Genus: Bicosoeca, Codonoeca, Histiona, Poteriodendron, Salpingoeca
- Family Bodonidae
Genus: Bodo, Cercomonas, Colponema, Phyllomitus, Pleuromonas, Rhynchomonas
Suborder Euchrysomonadina
- Family Ochromonadidae
Genus: Anthophysis, Cephalothamnium, Dendromonas, Monas, Stokesiella
- Family Multiciliidae
Genus: Multicilia
- Family Mastigamoebidae
Genus: Actinomonas, Dimorpha, Mastigamoeba, Mastigella, Pteridomonas
- Family Trimastigidae
Genus: Dallingeria, Macromastix
- Family Tetramitidae
Genus: Collodictyon, Costia, Tetramitus
- Family Hexamitidae
Genus: Hexaminta, Gyromonas, Trepomonas, Trigonomonas, Urophagus
Sarcodina
Class Rhizopoda
Order Testacida
- Family Gromiidae
Genus: Diplophrys, Gromia, Lecythium, Lieberkuhnia, Microgromia
- Family Arcellidae
Genus: Arcella, Chlamydophrys, ochliopodium, Difflugeilla, Diplochlamys, Hyalosphenia, Lesquereusia, Pamphagus, Pseudochlamys, Pyxidicula
- Family Difflugiidae
Genus: Amphitrema, Campascus, Centropyxis, Cucurbitella, Difflugia, Heleopera, Pontigulasia, Phryganella, Pseudodifflugia
- Family Euglyphidae
Genus: Assulina, Cyphoderia, Euglypha, Nebela, Placocista, Quadrulella, Sphenoderia, Trinema
Order Proteomyxida
- Family Labyrinthulidae
Genus: Labyrinthula
- Family Vampyrellidae
Genus: Biomyxa, Nuclearia, Vampyrella
- Family Pseudosporidae
Genus: Protomonas, Pseudospora
Order Amoebida
- Family Naegleriidae
Genus: Trimastigamoeba
- Family Amoebidae
Genus: Amoeba, Dinamoeba, Pelomyxa, Vahlkampfia
Class Actinopoda
- Family Actinocomidae
Genus: Actinocoma
- Family Actinophyridae
Genus: Actinophrys, Actinosphaerium
- Family Clathrulinidae
Genus: Clathrulina
- Family Myriophryidae
Genus: Myriophrys
- Family Lithocollidae
Genus: Lithocolla
- Family Heterophyridae
Genus: Heterophrys
- Family Acanthocystidae
Genus: Acanthocystis, Raphidiophrys