Archamoebea Cavalier-Smith 1983, sensu Cavalier-Smith et al. 2004

Diagnosis: Amoebae or ciliated amoebae, anaerobic or microaerophilic, free-living or endobionts of different invertebrate or vertebrate hosts; ciliated amoebae usually with hyaline lateral pseudopodia; unikont, with single kinetosome at the base of cilia, connected to the microtubular cone, in some cases both the kinetosome and the axoneme have atypical complements of microtubules; without typical mitochondria, in several cases mitochondrial derivates, i.e. mitosomes, have been demonstrated.

Mastigamoebida Frenzel 1897, sensu Cavalier-Smith 2013
Ciliated amoebaes or amoeboid organisms without cilia. The single motile anterior cilium, when present, associated with microtubular cone connected to the nucleus. Ciliated amoebaes with hyaline lateral pseudopodia.

Pelobiontida Page, 1976, sensu Cavalier-Smith 2013
Anaerobic or microaerophilic ciliated amoebae with slow-beating monokinetid or immobile polykinetids; ciliated amoebae often with hyaline lateral pseudopodia.

Mastigamoebaea Frenzel, 1892
Amoeboid with several pseudopodia; sometimes body without amoeboid motion, depending on conditions; single cilium directed forward, with vibrating beat; single kinetosome with cone of microtubules extending to nucleus; uninucleate, but some species multinucleate; large nucleoli persist through division with intranuclear spindle; stages without cilium occur; cysts; occurring in micro-aerophilic to anaerobic habitats rich in dissolved nutrients.
Incertae sedis Mastigamoebaea: Endolimax, Mastigina.

Entamoebidae Chatton, 1925, emend. Cavalier-Smith, 1993
Cilium and centrioles absent; with mitosomes instead of classical mitochondria; peroxisomes absent; mitosis closed with endonuclear centrosome and spindle; reduced Golgi dictyosome. Note that this diverse genus could potentially be subdivided into other genera. Entamoeba.

Tricholimax Frenzel 1897
Ciliated amoebae with single immobile cilium, microtubular cone associated with nucleus, when several nuclei present, each nucleus is connected to its own microtubular cone; with rhizostyle, derived from the lateral microtubular root.

Rhizomastix Alexeieff 1911
Diagnosis: Ciliate ciliated, possessing a rhizostyle arising from the basal body of the cilium and probably derived from the microtubular cone.