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)
- Infraclass Pteriomorphia (6 644)
- Superorder Eupteriomorphia
- Order Arcida (1 225)
- Order Colpomyida † (6)
- Order Cyrtodontida † (66)
- Order Limida (351)
- Order Myalinida † (576)
- Order Mytilida (707)
- Order Ostreida (705)
- Superfamily Ostreacea accepted as Ostreoidea Rafinesque, 1815
- Superfamily Ostreoidea Rafinesque, 1815 (243)
- Superfamily Pinnacea accepted as Pinnoidea Leach, 1819
- Superfamily Pinnoidea Leach, 1819 (138)
- Superfamily Pteriacea accepted as Pterioidea Gray, 1847 (1820)
- Superfamily Pterioidea Gray, 1847 (1820) (228)
- Family Anningellidae Hodges, 2022 †
- Family Aviculidae Goldfuss, 1820 accepted as Pteriidae J. E. Gray, 1847 (1820)
- Family Bakevelliidae W. King, 1850 † (36)
- Family Cassianellidae Ichikawa, 1958 † (8)
- Family Isognomonidae Woodring, 1925 (1828) (37)
- Genus Bathyisognomon Hickman, 2023 † (1)
- Genus Edentula L. Waagen, 1907 † accepted as Waagenoperna Tokuyama, 1959 †
- Genus Hippochaeta Philippi, 1844 † accepted as Isognomon (Hippochaeta) Philippi, 1844 †
- Genus Isognomon [Lightfoot], 1786 (31)
- Subgenus Isognomon (Anisoperna) Iredale, 1939 accepted as Isognomon [Lightfoot], 1786
- Subgenus Isognomon (Hippochaeta) Philippi, 1844 † represented as Isognomon [Lightfoot], 1786
- Subgenus Isognomon (Isognomon) [Lightfoot], 1786 represented as Isognomon [Lightfoot], 1786
- Subgenus Isognomon (Melina) Philipsson, 1788 accepted as Isognomon [Lightfoot], 1786
- Subgenus Isognomon (Parviperna) Iredale, 1939 represented as Isognomon [Lightfoot], 1786
- Species Isognomon acutirostris (Dunker, 1869) accepted as Isognomon nucleus (Lamarck, 1819)
- Species Isognomon acutirostris Otuka, 1936 accepted as Isognomon nucleus (Lamarck, 1819)
- Species Isognomon alatus (Gmelin, 1791)
- Species Isognomon albisoror (Iredale, 1939)
- Species Isognomon anomioides (Reeve, 1858) accepted as Isognomon australicus (Reeve, 1858)
- Species Isognomon attenuata (Reeve, 1858) accepted as Isognomon isognomum (Linnaeus, 1758)
- Species Isognomon australica (Reeve, 1858) accepted as Isognomon australicus (Reeve, 1858)
- Species Isognomon australicus (Reeve, 1858)
- Species Isognomon aviculare (Lamarck, 1819) accepted as Isognomon isognomum (Linnaeus, 1758)
- Species Isognomon bazini (Deshayes, 1858) †
- Species Isognomon bicolor (C. B. Adams, 1845)
- Species Isognomon brevirostre Link, 1807 accepted as Isognomon isognomum (Linnaeus, 1758)
- Species Isognomon californicum (Conrad, 1837) accepted as Isognomon californicus (Conrad, 1837)
- Species Isognomon californicus (Conrad, 1837)
- Species Isognomon ciscaucasica (Davitashvili, 1932) † accepted as Isognomon radiatus (M. Hörnes, 1867) †
- Species Isognomon dentifer (Krauss, 1848) accepted as Isognomon nucleus (Lamarck, 1819)
- Species Isognomon dunkeri (P. Fischer, 1881)
- Species Isognomon ephippium (Linnaeus, 1758)
- Species Isognomon fortissimus (L. C. King, 1933) †
- Species Isognomon gaudichaudi (A. d'Orbigny, 1843) †
- Species Isognomon incavatus (Cossmann, 1905) †
- Species Isognomon incisus (Conrad, 1837)
- Species Isognomon isognomon (Linnaeus, 1758) accepted as Isognomon isognomum (Linnaeus, 1758)
- Species Isognomon isognomum (Linnaeus, 1758)
- Species Isognomon janus P. P. Carpenter, 1857
- Species Isognomon lamarckii (Deshayes, 1830) †
- Species Isognomon legumen (Gmelin, 1791)
- Species Isognomon lilingensis R.-J. Zhang, 1977 †
- Species Isognomon lusitanicus (Sharpe, 1850) †
- Species Isognomon maxillatus (Lamarck, 1801) †
- Species Isognomon nucleus (Lamarck, 1819)
- Species Isognomon oneroaensis A. W. B. Powell & Bartrum, 1929 † accepted as Pteria oneroaensis (A. W. B. Powell & Bartrum, 1929) †
- Species Isognomon percrassa (Tate, 1899) †
- Species Isognomon perna (Linnaeus, 1767)
- Species Isognomon radiatus (Anton, 1838)
- Species Isognomon radiatus (M. Hörnes, 1867) †
- Species Isognomon recognitus (Mabille, 1895)
- Species Isognomon rekohuensis J. S. Crampton, 1988 †
- Species Isognomon ricordeanus (A. d'Orbigny, 1846) †
- Species Isognomon roberti H. J. Koch, 1953 accepted as Isognomon perna (Linnaeus, 1767)
- Species Isognomon rollei (M. Hörnes, 1867) †
- Species Isognomon rude (Reeve, 1858) accepted as Isognomon isognomum (Linnaeus, 1758)
- Species Isognomon rugosus (Münster, 1835) †
- Species Isognomon rupella (Dufo, 1840) accepted as Isognomon nucleus (Lamarck, 1819)
- Species Isognomon staadti (Cossmann, 1907) †
- Species Isognomon sulcatum (Lamarck, 1819) accepted as Isognomon perna (Linnaeus, 1767)
- Species Isognomon varnensis (Toula, 1892) †
- Species Isognomon vulsella (Lamarck, 1819) accepted as Isognomon legumen (Gmelin, 1791)
- Species Isognomon vulselloides Macsotay & Campos, 2001
- Species Isognomon wellmani J. S. Crampton, 1988 †
- Genus Tambanella Nakazawa & Newell, 1968 † (2)
- Genus Waagenoperna Tokuyama, 1959 † (3)
- Family Kochiidae Frech, 1891 † (1)
- Family Malleidae Lamarck, 1818 (14)
- Family Margaritidae Blainville, 1824 (21)
- Family Melinidae Meek & Hayden, 1865 accepted as Isognomonidae Woodring, 1925 (1828)
- Family Pedalionidae Stephenson, 1923 accepted as Pteriidae J. E. Gray, 1847 (1820)
- Family Pergamidiidae L. R. Cox, 1964 † (3)
- Family Pernidae J. Fleming, 1828 accepted as Isognomonidae Woodring, 1925 (1828)
- Family Plicatostylidae Lupher & E. L. Packard, 1929 † (6)
- Family Pteriidae J. E. Gray, 1847 (1820) (60)
- Family Pulvinitidae Stephenson, 1941 (6)
- Family Reniellidae Iredale, 1939 accepted as Pteriidae J. E. Gray, 1847 (1820)
- Family Vlastidae Neumayr, 1891 † (2)
- Family Vulsellidae J. E. Gray, 1854 (34)
- Superfamily Rhombopterioidea Korobkov, 1960 † (3)
- Family Pterineidae Meek, 1864 † (93)
- Order Pectinida (2 998)
- Order Pteriida accepted as Ostreida
- Order Pteriomorphia incertae sedis † (1)
- Superfamily Yunannioidea R.-J. Zhang & Z.-J. Niu, 2021 † (2)
- Family Ischyrodontidae Scarlato & Starobogatov, 1979 † (2)
- Family Matheriidae Scarlato & Starobogatov, 1979 † (1)
- Family Myodakryotidae Tunnicliff, 1987 † (4)
- 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