Flagellates with or without chloroplasts, phytomastigotes are possibly derived from secondary endosymbiosis of eukaryotic algae into the cells of zoomastigotes. Zoomastigophora Phytomastigophora

Codonosigidae
Codosiga or Codonosiga botrytis (11 samples)
Salpingoecidae
Salpingoeca (30 samples)
buetschlii (10), collaris (1), depressa (5), gracilis (4), urceolata (3), sp. 1-2 (7)

Diploeca (1)

Bicoecida

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Choanoflagellida

Bicoecida

Kinetoplastida

Cercomonadida

Rhizomastigida

Cryptophyceae

Dinophyceae

Euglenophyceae

Others

Zoomastigophora or Heterokonta/Chrysophyceae/Chromulinales Bicoecida (Bicosoecida)

Similar to Choanoflagellates, but vase-shaped lorica (or test) is made with chitinous materials

Bicoeca or Bicosoeca (Poteriodendron) petiolatum (3), sp.1-2 (4)
Histiona velifera (4)

Kinetoplastida

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Choanoflagellida

Bicoecida

Kinetoplastida

Cercomonadida

Rhizomastigida

Cryptophyceae

Dinophyceae

Euglenophyceae

Others

Zoomastigophora Kinetoplastida

One or two flagella emerging from a depression of cell body; with kinetoplast (feulgen-positive spherical or oval body at the base of flagellum)

Bodonidae
Bodo minimus (2), saltans (3), sp.1-6 (18)
Rhynchomomas nasuta (1), sp.1 (1)
Rhynchobodo sp.1 (2)
Cephalothamnium cyclopum (2), sp.1 (1)
Colponema loxodes (1)
Unidentified (2)

Cercomonadida

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Choanoflagellida

Bicoecida

Kinetoplastida

Cercomonadida

Rhizomastigida

Cryptophyceae

Dinophyceae

Euglenophyceae

Others

Zoomastigophora Cercomonadida

With two flagella of unequal length, no kinetoplast; flagellar base close to parabasal body

Cercomonas crassicauda (3), longicauda (1), sp.1-3 (19)

Rhizomastigida

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Choanoflagellida

Bicoecida

Kinetoplastida

Cercomonadida

Rhizomastigida

Cryptophyceae

Dinophyceae

Euglenophyceae

Others

Zoomastigophora Rhizomastigida

"Flagellated" amoeba

Mastigamoeba aspera (2), longfilum (2), sp.1-2 (2)
Mastigina (3)
Mastigella (1)

Unidentified sp.1-29 (55)

Cryptophyceae

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Choanoflagellida

Bicoecida

Kinetoplastida

Cercomonadida

Rhizomastigida

Cryptophyceae

Dinophyceae

Euglenophyceae

Others

Phytomastigophora Cryptophyceae or Cryptomonadida

Cell body kidney-shaped; two equal-length flagella emerged from anterior depression

Cryptomonadaceae (Cryptomonadidae)
Chroomonas sp. (19)
Cryptomonas (85)
erosa (2), ovata (10), platyuris (12), rostratiformis (9), tetrapyrenoidosa (4), sp.1-15 (48)

Chilomonas paramecium (34), sp.1-2 (6)　キロモナス
Goniomonas (Syn. Cyathomonas) truncata (13)

Dinophyceae

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Choanoflagellida

Bicoecida

Kinetoplastida

Cercomonadida

Rhizomastigida

Cryptophyceae

Dinophyceae

Euglenophyceae

Others

Phytomastigophora Dinophyceae or Dinoflagellida

Cell body with two grooves, horizontal and vertical; with or without chloroplasts;

Peridiniales

Peridinium (29 samples)

bipes (10), cunningtonii (1), elpatiewskyi (2), pygmaeum (2), volzii (6), sp.1-4 (8)

Scrippsiella trochoidea ? (1)
Ceratium furca (6), hirundinella (6)
Glenodinium (16 samples)

dinobryonis (2), pulvisculus (2), sp.1-5 (12)

Gymnodiniales

Gymnodinium (34 samples)
aeruginosum (4), carinatum (1), ordinatum (3), paradoxum (19), veris (2), sp.1-3 (5)

Gyrodinium (or Katodinium ?) sp. (3)
Hemidinium sp. 1-2 (3)

Unidentified sp.1-3 (5)

Dinococcales

Cystodinium ineris (6)

Noctilucales

Noctiluca sp.1 (1)

Euglenophyceae

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Choanoflagellida

Bicoecida

Kinetoplastida

Cercomonadida

Rhizomastigida

Cryptophyceae

Dinophyceae

Euglenophyceae

Others

Phytomastigophora Euglenophyceae or Euglenida

1 - 3 flagella emerging from anterior canal; with or without chloroplasts;

Eutreptiales

Eutreptia (or Diplonema ?) sp.1-2 (2)
Distigma sp.1 (1)

Euglenales

Euglena (703 samples)

acus (22), anabaena (16), archaeoplastidiata (3), bivittata (4), caudata (18), chadefaudii (1), clara (15), clavata (2), deses (87), ehrenbergii (35), fundoversata (3), gigas (10), gaumei (4), gracilis (17), granulata (10), hemichromata (25), limnophila (5), magnifica (6), mutabilis (87), oblonga (6), obtusa (6), oxyuris (22), pisciformis (=agilis, 37), polymorpha (1), proxima (8), rubra (1), sanguinea (12), schmitzii (11), sociabilis (5), spirogyra (79), stellata (6), tripteris (41), variabilis (4), viridis (49), wangi (4), sp.1-22 (40)

Phacus (284 samples)

acuminatus (45), aenigmaticus (11), brevicaudatus (2), caudatus (5), circulatus (4), curvicauda (9), gigas (3), hammeli (1), hispidulus (12), inflatus (3), landekiensis (6), lismorensis (4), longicauda (17), monilata (or suecicus) (2), obolus (7), pleuronectes (18), pyrum (30), pusillus (5), raciborskii (4), ranula (3), skujae (5), smulkowskianus (1), stokesii (14), torta (tortus or helikoides) (26), trapezoides (1), trimarginatus (2), triqueter (21), trypanon (8), undulatus (2), warszewiczii (2), sp.1-7 (11)

Lepocinclis (81 samples)

fusiformis (9), marssonii (9), ovum (25), salina (20), teres (1), wangi (8), sp.1-6 (9)

Colacium mucronatum (2), vesiculosum (4), sp.1 (1)
Strombomonas (10)

acuminata (2), borysteniensis (1), fluviatilis (5), fusiformis (1), gibberosa (1)

Trachelomonas (315 samples)

acanthostoma (1), abrupta (26), allia (15), armata (16), caudata (3), charkowiensis (1), crispa (3), cylindrica (10), dubia (1), dybowskii (13), granulosa (17), hexangulata (3), hispida (47), horrida (1), intermedia (11), klebsii (15), lacustris (7), oblonga (14), obtusa (1), ovoides (2), planktonica (2), playfairi (8), pulcherrima (7), pusilla (3), raciborski (3), robusta (2), rugulosa (1), scabra (8), similis (2), superba (9), volvocina (35), volzii (11), sp.1-13 (17)

Astasia klebsi (2), kathemerios (6), lagenula (8), longa (16), sp.1-3 (5)
Cyclidiopsis acus (15)

Rhabdomonadales

Rhabdomonas incurva (4), intermedia (2), sp.1-2 (3)
Menoidium gracile (8)

Sphenomonadales

Sphenomonas teres (8)
Calycimonas physaloides (37), sp.1-2 (3)
Petalomonas (14 samples) alata (2), asymmetrica (1), bicarinata (5), sp.1-5 (6)
Notosolenus (23 samples) apocamptus (8), ostium (2), sinuatus (4), sp.1-6 (9)
Anisonema (38 samples)

acinus (21), emarginatum (1), sp.1-6 (16)

Marsupiogaster sp. (6)
Dolium sp.1 (1)