Acanthopodina accepted as Discosea (source of synonymy)
Aconchulinida accepted as Vampyrellida (source of synonymy)
Ambermantidae Grimaldi, 2003 † (extant flag source)
Aporocotylidae Odhner, 1912 (habitat flag source)
Athalamea accepted as Monothalamea (source of synonymy)
Boraginales (extant flag source)
Buliminida accepted as Rotaliida (source of synonymy)
Choanogastraceae accepted as Pharyngomonadidae Cavalier-Smith, 2008 (source of synonymy)
Ciliatea accepted as Litostomatea (source of synonymy)
Conosea accepted as Variosea (source of synonymy)
Dermocystidae accepted as Rhinosporidiidae Mendoza, Ajello & Taylor, 2001 (source of synonymy)
Dinenymphaceae accepted as Pyrsonymphidae Grassi, 1892 (source of synonymy)
Filosa accepted as Reticulofilosa (source of synonymy)
Hematozoea accepted as Coccidiomorphea (source of synonymy)
Hypermastigida accepted as Trichonymphida (source of synonymy)
Kinetofragminophora accepted as Litostomatea (source of synonymy)
Leptothecata (extant flag source)
Mesomycetozoea accepted as Ichthyosporea (source of synonymy)
Occiusosporida accepted as Paramyxida (source of synonymy)
Perkinsida (habitat flag source)
Postgaardida (habitat flag source)
Postgaardida (extant flag source)
Proteomyxidea accepted as Gromiidea (source of synonymy)
Rhizopoda accepted as Sarcomastigota (source of synonymy)
Salmoniformes incertae sedis (extant flag source)
Silicoloculinida accepted as Miliolida (source of synonymy)
Spongomonadea accepted as Imbricatea (source of synonymy)
Stellatosporea accepted as Ascetosporea (source of synonymy)
Testaceafilosea accepted as Imbricatea (source of synonymy)
Xenophyophorea accepted as Monothalamea (source of synonymy)