Between brackets is the number of accepted species
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- Mollusca (133 221)
- Subphylum Aculifera
- Subphylum Conchifera
- Subphylum Placophora accepted as Polyplacophora
- Superclass Aplacophora
- Class Amphineura accepted as Aculifera
- Class Bivalvia (25 077)
- Subclass Autobranchia (23 354)
- Infraclass Heteroconchia (16 679)
- Subterclass Archiheterodonta (1 210)
- Subterclass Euheterodonta (11 394)
- Superorder Anomalodesmata (990)
- Order Laternulacea accepted as Thracioidea Stoliczka, 1870 (1839)
- Suborder Laternulina accepted as Thracioidea Stoliczka, 1870 (1839)
- Suborder Septibranchia
- Superfamily Anomalodesmata incertae sedis (4)
- Superfamily Clavagelloidea A. d'Orbigny, 1844 (34)
- Superfamily Cuspidarioidea Dall, 1886 (334)
- Superfamily Myochamoidea P. P. Carpenter, 1861 (55)
- Family Chamostreidae Stoliczka, 1870 accepted as Cleidothaeridae Hedley, 1918 (1870)
- Family Cleidothaeridae Hedley, 1918 (1870) (4)
- Family Myochamidae P. P. Carpenter, 1861 (51)
- Genus Hunkydora C. A. Fleming, 1948 (4)
- Genus Myadora Gray, 1840 (35)
- Genus Myadoropsis Habe, 1960 (5)
- Species Myadoropsis brevispinosa Habe, 1962
- Species Myadoropsis dissimilis Habe, 1960
- Species Myadoropsis elongata (May, 1915)
- Species Myadoropsis transmontana (Yokoyama, 1922)
- Species Myadoropsis wairua B. A. Marshall, 2002
- Genus Myochama Stutchbury, 1830 (7)
- Genus Myodora [sic] accepted as Myadora Gray, 1840
- Genus Myodoropsis [sic] accepted as Myadoropsis Habe, 1960
- Superfamily Pandoroidea Rafinesque, 1815 (86)
- Superfamily Pholadomyoidea W. King, 1844 (62)
- Superfamily Poromyoidea Dall, 1886 (78)
- Superfamily Thracioidea Stoliczka, 1870 (1839) (189)
- Superfamily Verticordioidea Stoliczka, 1870 (148)
- Family Cercomyidae Crickmay, 1936 † accepted as Laternulidae Hedley, 1918 (1840)
- Superorder Imparidentia (10 371)
- Order Anomalodesmacea accepted as Anomalodesmata
- Order Euheterodonta incertae sedis (27)
- Order Pholadomyida represented as Anomalodesmata
- Family Lipanellidae T. M. Sánchez, 2005 † (4)
- Family Rhaetidiidae Dominici & Danise, 2024 † (2)
- Subterclass Heterodonta
- Subterclass Palaeoheterodonta (4 074)
- Superorder Heteroconchia incertae sedis † (1)
- Infraclass Pteriomorphia (6 675)
- Subclass Bivalvia incertae sedis (7)
- Subclass Palaeotaxodonta accepted as Nuculida
- Subclass Paleoheterodonta accepted as Palaeoheterodonta
- Subclass Protobranchia (1 374)
- Infraclass Cryptodonta † (342)
- Class Caudofoveata (143)
- Class Cephalopoda (1 917)
- Class Conchifera accepted as Bivalvia
- Class Cricoconarida † (1)
- Class Gastropoda (102 971)
- Class Lamellibranchiata accepted as Bivalvia
- Class Loricata accepted as Polyplacophora
- Class Mollusca incertae sedis † (372)
- Class Monoplacophora (229)
- Class Pelecypoda accepted as Bivalvia
- Class Polyplacophora (1 381)
- Class Polyplaxiphora accepted as Polyplacophora
- Class Rostroconchia † (64)
- Class Scaphopoda (753)
- Class Solenoconchia accepted as Scaphopoda
- Class Solenogastres (313)
- Subclass Chaetodermomorpha accepted as Caudofoveata
