Between brackets is the number of accepted species

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- Mollusca (133 121)
- Subphylum Aculifera
- Subphylum Conchifera
- Subphylum Placophora accepted as Polyplacophora
- Superclass Aplacophora
- Class Amphineura accepted as Aculifera
- Class Bivalvia (25 074)
- Subclass Autobranchia (23 351)
- Infraclass Heteroconchia (16 678)
- Subterclass Archiheterodonta (1 210)
- Subterclass Euheterodonta (11 393)
- Superorder Anomalodesmata (990)
- Superorder Imparidentia (10 370)
- Order Adapedonta (263)
- Order Cardiida (3 058)
- Order Galeommatida (791)
- Order Gastrochaenida (43)
- Order Hiatellida represented as Adapedonta
- Order Hippuritida † (322)
- Order Lucinida (998)
- Order Megalodontida † (141)
- Order Modiomorphida † (95)
- Order Myacea accepted as Myida
- Order Myida (925)
- Order Sphaeriida (662)
- Superfamily Sphaerioidea Deshayes, 1855 (1820) (662)
- Family Corneocycladidae Hannibal, 1912 accepted as Sphaeriidae Deshayes, 1855 (1820)
- Family Euglesidae Pirogov & Starobogatov, 1974 accepted as Sphaeriinae Deshayes, 1855 (1820)
- Family Kijidae C. M. Kolesnikov, 1977 † (21)
- Family Limnocyrenidae C. M. Kolesnikov, 1977 † (39)
- Family Neomiodontidae R. Casey, 1955 † (122)
- Subfamily Eomiodontinae Hayami, 1965 † accepted as Neomiodontidae R. Casey, 1955 †
- Genus Amphiaraus H. E. Vokes, 1946 † accepted as Eomiodon L. R. Cox, 1935 †
- Species Amphiaraus seleniscus H. E. Vokes, 1946 † accepted as Eomiodon seleniscus (H. E. Vokes, 1946) †
- Genus Bidentina Oppenheim, 1895 † accepted as Neomiodon P. Fischer, 1887 †
- Genus Costocyrena R. Casey, 1955 † (9)
- Genus Costocyrena Hayami, 1965 † accepted as Costocyrena R. Casey, 1955 †
- Genus Crenotrapezium Hayami, 1958 † (3)
- Genus Cyrenopsis Etheridge, 1902 † (4)
- Genus Dianina F.-X. Guo, 1985 † (3)
- Genus Eomiodon L. R. Cox, 1935 † (27)
- Genus Eosion F.-X. Guo, 1988 † (1)
- Genus Gansuella Q.-H. Ma, 1986 † (4)
- Genus Mifunea Tamura, 1977 † (1)
- Genus Miodon F. Sandberger, 1870 † accepted as Neomiodon P. Fischer, 1887 †
- Genus Musculiopsis MacNeil, 1939 † (7)
- Genus Myrene R. Casey, 1955 † (24)
- Genus Neomiodon P. Fischer, 1887 † (30)
- Genus Neomiodonoides Q.-H. Ma, 1986 † (7)
- Genus Neomyrene Koarai & Matsukawa, 2016 † accepted as Myrene (Mesocorbicula) K. Suzuki & Oyama, 1943 †
- Genus Protocyprina H. E. Vokes, 1946 † accepted as Eomiodon L. R. Cox, 1935 †
- Genus Protomiodon F. W. Anderson & L. R. Cox, 1948 † accepted as Neomiodon P. Fischer, 1887 †
- Genus Pseudasaphis Matsumoto, 1938 † (1)
- Genus Subtilia C. M. Kolesnikov, 1980 † (1)
- Family Pisidiidae Gray, 1857 accepted as Sphaeriidae Deshayes, 1855 (1820)
- Family Sibireconchidae C. M. Kolesnikov, 1977 † (3)
- Family Sphaeriidae Deshayes, 1855 (1820) (477)
- Family Starobogatoviconchidae Zykin †
- Order Venerida (2 826)
- Superfamily Cyamioidea G. O. Sars, 1878 (98)
- Superfamily Gaimardioidea Hedley, 1916 accepted as Cyamioidea G. O. Sars, 1878
- Superfamily Galeommatacea accepted as Galeommatoidea J. E. Gray, 1840
- Superfamily Grammysioidea S. A. Miller, 1877 † (102)
- Superfamily Kalenteroidea Marwick, 1953 † (46)
- Superfamily Mactracea accepted as Mactroidea Lamarck, 1809
- 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 (6 673)
- 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 (1 864)
- Class Conchifera accepted as Bivalvia
- Class Cricoconarida † (1)
- Class Gastropoda (102 927)
- 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