- Ebriophyceae
- Echinamoeba Page, 1975
- Echinamoebida
- Echinamoebida incertae sedis
- Echinosteliida
- Echinostelium De Bary, 1855
- Eisenackidium F.H.Cramer & M.del C.Díez de Cramer, 1968
- Ellisiella Norton, 1965
- Embryocola Michajlow, 1969
- Endolimax Kuenen & Swellengrebel, 1913
- Endostelium Olive, Bennett & Deasey, 1984
- Entamoeba Casagrandi & Barbagallo, 1897
- Entamoebidae Chatton, 1925, emend. Cavalier-Smith, 1993
- Enteromonadia
- Enteromonadida
- Enteromonadidae Kulda & Nohýnková, 1978
- Entosiphon Stein, 1878
- Eopharyngia
- Eotuberitina
- Eozoa
- Ephelopalla Wicander
- Estiastra A.Eisenack, 1959
- Euamoebida
- Euamoebida incertae sedis
- Eubodonida
- Euglena Ehrenberg, 1830
- Euglenaceae
- Euglenaria
- Euglenia
- Euglenida
- Euglenocapsa F.Steinecke
- Euglenoidea
- Euglenoidea
- Euglenoidea incertae sedis
- Euglenomonas Skvortzov & M.Noda, 1983
- Euglenopsis Klebs, 1892
- Euglenosoma H.S.Davis
- Euglenostigmanopsis Skvortzov & M.Noda
- Euglenozoa (koljeno)
- Euglenozoa podcarstvo)
- Eulophomonas G.B.Grassi, 1911
- Eupoikilofusa F.H.Cramer, 1970
- Eutreptia Perty, 1852
- Eutreptiaceae Hollande, 1942
- Eutreptiella A.da Cunha, 1914
- Eutreptiida
- Excavata