[ref. ID; 4944 (Thomas Cavalier-Smith, Ema E.-Y.Chao, Brian Oates, 2004)]

Phylum Amoebozoa Luhe 1913 stat. nov. Corliss 1984 emend. Cavalier-Smith 1998
Revised diagnosis: Ancestrally unikont and aerobic eukaryotes, typically with a single kinetid per cell with only one centriole associated with the apex of a cone of microtubules or (usually) secondarily non-ciliate and non-centriolar; rarely (Multicilia, Pelomyxa, some protostelids) multiciliate with monokinetids; rarely secondarily biciliate with plasmodial as well as amoeba and flagellate stages (Myxogastrea); non-ciliate forms and some ciliated forms undergo amoeboid motion, using pseudopods that are typically lobose or lamellipodial (with or without pointed or blunt subpseudopodia); true filopodia (i.e. ones able to attach to surfaces and draw the cell forwards) absent; mitochondria with usually branched tubular cristae or reduced to tiny non-cristate mitosomes; stacked Golgi dictyosomes obvious in aerobic, but not in most anaerobic species.

Subphylum 1. Protamoebae Cavalier-Smith subphyl. nov.
Diagnosis: Amoebae with Golgi dictyosomes; fruiting bodies typically absent, when rarely present (Copromyxida) without stalk tube; typically aerobic (except for breviates); mitochondria with branched tubular cristae.

Class 1. Breviatea Cavalier-Smith cl. nov.
Diagnosis: Uniciliate anaerobic amoebae distinguished from Archamoebae by cilium being shorter than body and lacking their rRNA signatures
Etymology: L. brevis, short referring to the short cilium, to the unusually short branches of this taxon on rRNA trees compared with other Amoebozoa, and to the fact that its rRNA is the shortest of any Amoebozoa, in contrast to ciliated Archamoebae, which have the longest. The vernacular term 'breviates' is appropriate for the group; I am aware that 'breviate' also means 'a summary' or 'lawyers brief', but it is virtually obsolete in both senses, so no confusion should arise from this novel usage.
Order Breviatida Cavalier-Smith ord. nov.
Diagnosis: As for the class (e.g., 'Mastigamoeba invertens')

Class 2. Lobosea Carpenter 1861 emend.
Diagnosis: Aerobic uninucleate amoebae, lacking glycostyles or scales; locomotion by monopodial or polypodial lobose pseudopods that were ancestrally cylindrical and non-eruptive, but are sometimes flattened or eruptive; lack cilia or centrosomes; often with very thick glycocalyx; pointed protoplasmic projections absent, or if present (Echinamoeba only) much sparser than in acanthamoebids, Filamoeba or Mycetozoa; open mitosis.

Order 1. Euamoebida Lepsi emend. Lobosea without tests or fruiting bodies
Superfamily 1. Amoeboidea Ehrenberg stat. nov.
Diagnosis: Aerobic amoebae with non-eruptive cylindrical lobose pseudopods
Type genus: Amoeba
Family 1. Amoebidae Ehrenberg 1838 (e.g., Amoeba, Chaos, Saccamoeba, Polychaos)
Family 2. Hartmannellidae Volkonsky 1931 (e.g., Hartmannella, Cashia, Glaeseria)

Superfamily 2. Echinamoeboidea page stat. nov.
Diagnosis: flattened irregular aerobic amoebae often with sparse short spine-like subpseudopodia; cysts with single-layered walls, with or without pores closed by opercula.
Type genus; Echinamoeba
Family Echinamoebidae Page 1975 (Echinamoeba)

Superfamily 3. Leptomyxoidea Pussard and Pons 1976 stat. nov.
Family 1. Flabellulidae Bovee 1970 (Paraflabellula)
Family 2. Leptomyxidae Pussard and Pons 1976 (Leptomyxa, Rhizamoeba)

Order 2. Copromyxida Cavalier-Smith 1993 (with fruiting bodies)
Family 1. Copromyxidae Olive & Stoianovitch 1975 (Copromyxa, Copromyxella)

Order 3. Arcellinida Kent 1880
Suborder 1. Arcellinina: Haeckel 1884 (3 families)
Suborder 2. Difflugiina: Meisterfeld 2002 (13 families)
Suborder 3. Phryganellina: Bovee, 1985 (2 families)

Class 3. Discosea Cavalier-Smith cl. nov.
Diagnosis: Strongly flattened amoebae with leading lamellipodium with or without subpseudopodia; non-eruptive movement; usually with glycostyles, organic scales or very thick amorphous coat; mostly monopodial and uninucleate,
Etymology: L. discus a disc; a meaningless euphonious suffix as in Lobosea and Conosa.

Order 1. Glycostylida Cavalier-Smith ord. nov.
Diagnosis: Aerobic uninucleate amoebae ancestrally with surface coat of hexagonal glycostyles (vexilliferids) or other hexagonal filamentous glycocalyx components in Platyamoeba, putatively modified to pentagonal glycostyles in Vannella or fenestrated scales in many paramoebids; non-ciliate with no centrosome or (rarely) with numerous cilia with unicentriolar kinetid.
Superfamily 1. Vannelloidea Bovee stat. nov.
Diagnosis: Ancestrally with typically pentagonal glycostyles and cilia (often lost); lamellipodium without dactylopodia; parasomes absent.
Type genus: Vannella
Family 1. Vannellidae Bovee 1970 (Vannella, Platyamoeba, Lingulamoeba, Clydonella)
Family 2. Multiciliidae Poche 1913
Revised diagnosis: Weakly amoeboid multiciliate cells with unicentriolar kinetids over the whole cell surface; mitochondria with tubular cristae; surface glycostyles; centrioles surrounded by inverted truncated microtubular cones interconnected by cortical microtubular bands. (Multicilia)

Superfamily 2. Paramoeboidea Poche 1913 stat. nov.
Diagnosis: non-ciliate; with dactylopodia and parasomes.
Type genus: Paramoeba
Family 1. Vexilliferidae Page 1987 (Vexillifera, Neoparamoeba)
Family 2. Paramoebidae Poche 1913 (e.g., Paramoeba, Mayorella, Korotnevella)

Order 2. Himatismenida Page 1987 (dorsal organic scales)
Family Cochliopodiidae De Saedeleer 1934 (Cochliopodium, Gocevia, Paragocevia)

Order 3. Dermamoebida Cavalier-Smith ord. nov.
Diagnosis: Aerobic uninucleate, or sometimes bi- or multinucleate, amoebae with thick, usually amorphous glycocalyx lacking scales or glycostyles; antero-posteriorly elongated discs moving by a broad crescent-shaped lamellipodium
Family Thecamoebidae Schaeffer 1926 (e.g., Dermamoeba, Thecamoeba)

Discosea incertae sedis: Family Hyalodiscidae Poche 1913 (e.g., Hyalodiscus)

Class 4. Variosea Cavalier-Smith cl. nov.
Diagnosis: Cells ancestrally with a single centriole and cilium and resting cyst, no fruiting body or locomotory lamellipodia; typically with many subpseudopodia, pointed or broad but non-eruptive (in latter case cell appearing branched) pseudopodia or branched pseudopods; mitochondria with branched cristae; cilium usually absent, in which case a lamellate centrosome is often present.
Etymology: L. varis diverse, various; a meaningless euphonious suffix as in Lobosea and Conosa. Emphasizes their exceptionally varied phenotype compared with the other 3 classes of Protamoebae, with some species amoebae (with or without centrosomes) and others flagellates, some with thin, pointed pseudopodia and others with broad blunt ones, some with branched pseudopods and some with anastomosing ones.

Order 1. Phalansteriida Hibberd 1983
Family Phalansteriidae Kent 1880/1 emend. (Phalansterium)

Order 2. Centramoebida Rogerson & Patterson 2002 emend. (the name was first suggested by Patterson (1994) without diagnosis but with a circumscription that included also Stereomyxidae and Dictyosteliida but excluded Balamuthia).
Emended diagnosis: Cells and cyst wall tripartite; inner endocyst is undulated, in places well separated by a low density mesocyst from the exocyst, but in contact in places giving the cyst wall a ridged appearance in surface view; usually with lamellate centrosome- exception Comandonia.
Family 1. Acanthamoebidae Sawyer & Griffin 1971 (pointed subpseudopodia) (Acanthamoeba, Comandonia, Protacanthamoeba)
Family 2. Balamuthiidae Cavalier-Smith fam. nov.
Diagnosis: lobose pseudopodia without pointed subpseudopodia
Type genus: Balamuthia Visvesvara et al., 1993

Order 3. Varipodida Cavalier-Smith ord. nov.
Diagnosis: Branched non-ciliate flattened amoebae without cilia or centrosomes and cysts with smooth single-layered walls; with non-plasmodial branched cells with broad non-eruptive pseudopods.
Family 1. Gephyramoebidae Pussard & Pons 1976 (Gephyramoeba)
Family 2. Filameobidae Cavalier-Smith fam. nov.
Diagnosis: flattened fan-shaped aerobic free-living amoebae with numerous slender pointed filiform pseudopodia arising from the hyaline edge; fruiting bodies, cilia, centrioles, sales or glycostyles absent; ovoid cysts with smooth single-layered thick wall.
Type genus: Filamoeba Page 1967

Variosea incertae sedis: Family Stereomyxidae Grell 1966 (Stereomyxa, Corallomyxa) (slender branched pseudopodia, tapering but blunt-tipped, sometimes anastomosing; marine; lamellate centrosome, no cilia or centrioles)

Subphylum 2. Conosa Cavalier-Smith 1998
Infraphylum 1. Archamoebae Cavalier-Smith 1983 stat. nov. 1998
Class Archamoebae Cavalier-Smith 1983 stat. nov.
Order 1. Pelobiontida Page 1976 (with amoeboid motion; amoeboid phases dominate the life cycle)
Family 1. Pelomyxidae Schulze 1977 (Pelomyxa, Mastigina)
Family 2. Entamoebidae Chatton 1925 (Entamoeba)

Order 2. Mastigamoebida Frenzel 1982 em.
Family 1. Mastigamoebidae Goldschmidt 1907 (swimming flagellates typically lacking amoeboid motion) (Mastigamoeba, Mastigella, Phreatamoeba)
Family 2. Endolimacidae Cavalier-Smith fam. nov.
Diagnosis: flattish amitochondrial monopodial amoebae with eruptive pseudopodia; intestinal commensals lacking cilia, centrioles, contractile vacuoles or intracellular crystals.
Type genus: Endolimax Kuenen & Swellengrebel 1913 (Endamoeba)

Infraphylum 2. Mycetozoa De Bary 1873 stat. nov. Cavalier-Smith 1988 (pseudopods usually acutely pointed, typically with stalked sorocarps; ciliate stages ancestrally with outer cone of microtubules underlying the cell surface and inner cone attached to a central fibrous centriolar root)
Class 1. Stelamoeba Cavalier-Smith cl. nov.
Diagnosis: Minute fruiting bodies (sorocarps) arise from single amoebae or aggregates of amoebae; sorocarps comprise a sorus of one to many spores borne on a cellulosic stalk tube; amoebae with pointed pseudopods; with one to several unikont (unicentriolar) cilia or non-ciliate; non-ciliate amoebae with an elaborate cytoplasmic microtubular skeleton in interphase (Guhl & Roos, 1994); spores are exospores formed by migrating amoebae, not endogenously by subdivision within plasmodia as in Myxogastrea.

Order 1. Protostelida Olive & Stoianovitch 1966 emend.
Revised diagnosis: Minute fruiting bodies (sorocarps) arise from single amoebae; ciliated phases when present with single centrioles.
Family 1. Protosteliidae Olive & Stoianovitch 1966 (e.g., Protostelium, Schizoplasmodium)
Family 2. Cavosteliidae Olive & Stoianovitch 1964 (e.g., Cavostelium, Planoprotostelium)

Order 2. Dictyosteliida Lister 1909 or Olive 1970
Family 1. Acytosteliidae Raper in Raper and Quinlan 1958 (Acytostelium)
Family 2. Dictyosteliidae Rostafinski 1875 (Dictyostelium, Polysphondylium, Coenonia)

Class 2. Myxogastrea Fries 1829 stat. nov. Cavalier-Smith 1993 emend.
Diagnosis: With lamellipoidal/filopodial amoeba, flagellate, and (usually) Plasmodial phases; flagellate phase with two centrioles, each with two microtubular bands, biciliate or sometimes uniciliate; mitochondria typically with central rod-shaped nucleoid; with multilayered cysts or with spores (developing within the plasmodia) borne on fruiting bodies; flagellate stage with inner microtubular cone attached apically to a microtubule nucleatig centre at the end of a fibrillar root emanating from the anterior centriolar base.

Order 1. Parastelida Cavalier-Smith ord. nov.
Diagnosis: Minute fruiting bodies (sorocarps) arise from single amoebae, aggregates of amoebae or microscopic plasmodia; distinguished from other Myxogastrea by having only 1-4 spores on a very delicate stalked sorocarp.
Family 1. Ceratiomyxidae Schroter 1889 (Ceratiomyxa, Ceratiomyxella)

Order 2. Echinosteliida Keller & Brooks 1976
Family 1. Echinosteliidae Rostafinski 1873 (Echinostelium)
Family 2. Clastodermidar Alexopouls and Brooks 1971 (Barbeyella, Clastoderma)

Order 3. Liceida Jahn 1928 (3 families: Listerellidae Jahn, 1928; Liceidae Rostafinski, 1873; Enteriidae Farr, 1982)

Order 4. Trichiida Macbride (1922) (2 families: Dianemidae Macbride, 1899; Trichiidae Rostafinski, 1873)

Order 5. Stemonitida Macbride 1922 (Stemonitidae Rostafinski, 1873, e.g., Stemonitis)

Order 6. Physarida Macbride 1922
Family 1. Elaeomyxidae Hagelstein 1982 (Elaeomyxa)
Family 2. Physaridae Rostafinski 1873 (e.g., Physarum, Badhamina, Fuligo)
Family 3. Didymiidae Rostafinski 1873 (e.g., Didymium)

Myxogastrea incertae sedis: "Echinostelium" bisporum (ultrastructure as Cladostelium bisporum (Furtago and Olive, 1970)); Hyperamoeba spp. aggregate

Mycetozoa incertae sedis: Family Echinosteliopsidae (Echinosteliopsis)
The order Trichosida Mobius 1889, family Trichosidae Mobius, 1889 (Trichosphaerium) is here provisionally excluded from Amoebozoa on the basis of early reports of a biciliate stage (Schaudinn, 1899; Minchin, 1922); such a stage, although not mentioned by recent authors (Page, 1983), if present would suggest, together with the complex multiphasic life cycle, that this genus may belong among the bikont Rhizaria (Cavalier-Smith, 2002) rather than in the Amoebozoa. Whether its curious lobose pseudopods are related to those of Lobosea or not is unclear, though they are more suggestive of a position within Protamoebae than within Rhizaria.