Between brackets is the number of accepted species

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- Mollusca (132 738)
- Subphylum Aculifera
- Subphylum Conchifera
- Subphylum Placophora accepted as Polyplacophora
- Superclass Aplacophora
- Class Amphineura accepted as Aculifera
- Class Bivalvia (24 984)
- Subclass Autobranchia (23 270)
- Infraclass Heteroconchia (16 634)
- Subterclass Archiheterodonta (1 205)
- Subterclass Euheterodonta (11 356)
- Superorder Anomalodesmata (987)
- Superorder Imparidentia (10 336)
- Order Adapedonta (260)
- Order Cardiida (3 055)
- Order Galeommatida (791)
- Order Gastrochaenida (43)
- Order Hiatellida represented as Adapedonta
- Order Hippuritida † (321)
- Order Lucinida (997)
- Order Megalodontida † (141)
- Order Modiomorphida † (94)
- Order Myacea accepted as Myida
- Order Myida (924)
- 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)
- Family Pisidiidae Gray, 1857 accepted as Sphaeriidae Deshayes, 1855 (1820)
- Family Sibireconchidae C. M. Kolesnikov, 1977 † (3)
- Family Sphaeriidae Deshayes, 1855 (1820) (477)
- Subfamily Euglesinae Pirogov & Starobogatov, 1974 accepted as Sphaeriinae Deshayes, 1855 (1820)
- Subfamily Euperinae Heard, 1965 (43)
- Genus Byssanodonta A. d'Orbigny, 1846 (2)
- Genus Eupera Bourguignat, 1854 (41)
- Subfamily Lacustrininae Korniushin, 1989 accepted as Sphaeriinae Deshayes, 1855 (1820)
- Subfamily Musculiinae Starobogatov, 1984 accepted as Sphaeriidae Deshayes, 1855 (1820)
- Subfamily Neopisidiinae Korniushin, 1989 accepted as Sphaeriinae Deshayes, 1855 (1820)
- Subfamily Pisidiinae Gray, 1857 accepted as Sphaeriinae Deshayes, 1855 (1820)
- Subfamily Sphaeriinae Deshayes, 1855 (1820) (424)
- Tribe Euglesini Pirogov & Starobogatov, 1974 accepted as Sphaeriinae Deshayes, 1855 (1820)
- Genus Amesoda Rafinesque, 1820 accepted as Sphaerium (Amesoda) Rafinesque, 1820
- Genus Cordula Leach, 1852 accepted as Pisidium C. Pfeiffer, 1821
- Genus Megasphaerioides Komatsu, J.-H. Chen & Q.-F. Wang, 2003 † (1)
- Genus Pera Leach, 1831 accepted as Pisidium C. Pfeiffer, 1821
- Genus Pisum Megerle von Mühlfeld, 1811
- Genus Protosphaerium Hocknull, 2000 † (2)
- Genus Sphaericoncha C. M. Kolesnikov, 1980 † (4)
- Genus Sphaerinova Iredale, 1943 accepted as Musculium (Sphaerinova) Iredale, 1943
- Genus Sphaerioides J.-S. Yu & K. Zhang, 1982 † (3)
- Genus Tetoriunio Koarai & Matsukawa, 2016 † accepted as Megasphaerioides Komatsu, J.-H. Chen & Q.-F. Wang, 2003 †
- Family Starobogatoviconchidae Zykin †
- Order Venerida (2 821)
- 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 † (90)
- Superfamily Kalenteroidea Marwick, 1953 † (39)
- 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 (4 072)
- Superorder Heteroconchia incertae sedis † (1)
- Infraclass Pteriomorphia (6 636)
- Subclass Bivalvia incertae sedis (7)
- Subclass Palaeotaxodonta accepted as Nuculida
- Subclass Paleoheterodonta accepted as Palaeoheterodonta
- Subclass Protobranchia (1 365)
- Infraclass Cryptodonta † (342)
- Class Caudofoveata (143)
- Class Cephalopoda (1 830)
- Class Conchifera accepted as Bivalvia
- Class Cricoconarida † (1)
- Class Gastropoda (102 673)
- 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 (1 377)
- Class Polyplaxiphora accepted as Polyplacophora
- Class Rostroconchia † (64)
- Class Scaphopoda (752)
- Class Solenoconchia accepted as Scaphopoda
- Class Solenogastres (313)
- Subclass Chaetodermomorpha accepted as Caudofoveata