Between brackets is the number of accepted species

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- Mollusca (132 754)
- Subphylum Aculifera
- Subphylum Conchifera
- Subphylum Placophora accepted as Polyplacophora
- Superclass Aplacophora
- Class Amphineura accepted as Aculifera
- Class Bivalvia (24 992)
- Subclass Autobranchia (23 278)
- 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)
- Order Venerida (2 821)
- Superfamily Arcticoidea R. B. Newton, 1891 (1844) (67)
- Superfamily Chamoidea Lamarck, 1809 (105)
- Superfamily Corbiculoidea J. E. Gray, 1847 accepted as Cyrenoidea J. E. Gray, 1840
- Superfamily Cyrenoidea J. E. Gray, 1840 (441)
- Superfamily Cyrenoidoidea H. Adams & A. Adams, 1857 (1853) accepted as Cyrenoidea J. E. Gray, 1840
- Superfamily Glossoidea J. E. Gray, 1847 (1840) (218)
- Superfamily Hemidonacoidea Scarlato & Starobogatov, 1971 (7)
- Superfamily Mactroidea Lamarck, 1809 (372)
- Family Anatinellidae J. E. Gray, 1853 (12)
- Family Cardiliidae P. Fischer, 1887 (10)
- Family Mactridae Lamarck, 1809 (315)
- Family Mesodesmatidae J. E. Gray, 1840 (35)
- Genus Amarilladesma M. Huber, 2010 (1)
- Genus Amesodesma Iredale, 1930 accepted as Paphies (Amesodesma) Iredale, 1930
- Genus Anapella Dall, 1895 (3)
- Genus Atactodea Dall, 1895 (6)
- Genus Caecella accepted as Coecella J. E. Gray, 1853
- Genus Ceronia J. E. Gray, 1853 accepted as Mesodesma (Ceronia) J. E. Gray, 1853
- Genus Coecella J. E. Gray, 1853 (4)
- Species Coecella chinensis Deshayes, 1855
- Species Coecella erythrodon (Lamarck, 1818) accepted as Corbula erythrodon Lamarck, 1818
- Species Coecella formosae de Rooij-Schuiling, 1972
- Species Coecella horsfieldii Gray, 1853
- Subspecies Coecella horsfieldii formosae de Rooij-Schuiling, 1972 accepted as Coecella formosae de Rooij-Schuiling, 1972
- Species Coecella qeratensis S. Morris & N. Morris, 1993
- Genus Davila J. E. Gray, 1853 (1)
- Genus Donacilla R. A. Philippi, 1836 (2)
- Genus Donacilla Blainville, 1819
- Genus Eryx Mörch, 1853 accepted as Atactodea Dall, 1895
- Genus Machaena J. E. Gray, 1843 accepted as Paphies R. P. Lesson, 1831
- Genus Mesodesma Deshayes, 1832 (3)
- Genus Monterosatus Beu, 1971 accepted as Planktomya Simroth, 1896
- Genus Paphia Lamarck, 1799 accepted as Atactodea Dall, 1895
- Genus Paphies R. P. Lesson, 1831 (13)
- Genus Regterenia Rooij-Schuiling, 1972 (1)
- Genus Soleilletia Bourguignat, 1885 (1)
- Genus Taria J. E. Gray, 1853 accepted as Paphies (Taria) J. E. Gray, 1853
- Family Rangiidae P. Fischer, 1884 accepted as Mactridae Lamarck, 1809
- Superfamily Opokielloidea Kanev, 1983 † (10)
- Superfamily Palaeanodontoidea Modell, 1964 † accepted as Palaeomuteloidea Lahusen, 1897 †
- Superfamily Prilukielloidea Starobogatov, 1970 † (59)
- Superfamily Ungulinoidea J. E. Gray, 1854 (159)
- Superfamily Veneracea accepted as Veneroidea Rafinesque, 1815
- Superfamily Veneroidea Rafinesque, 1815 (1 383)
- 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 (6 644)
- 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 (1 832)
- Class Conchifera accepted as Bivalvia
- Class Cricoconarida † (1)
- Class Gastropoda (102 679)
- 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