Between brackets is the number of accepted species

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- Mollusca (132 851)
- Subphylum Aculifera
- Subphylum Conchifera
- Subphylum Placophora accepted as Polyplacophora
- Superclass Aplacophora
- Class Amphineura accepted as Aculifera
- Class Bivalvia (25 013)
- Subclass Autobranchia (23 299)
- Infraclass Heteroconchia (16 639)
- Infraclass Pteriomorphia (6 660)
- Superorder Eupteriomorphia
- Order Arcida (1 227)
- Order Colpomyida † (6)
- Order Cyrtodontida † (66)
- Order Limida (358)
- Order Myalinida † (576)
- Order Mytilida (707)
- Order Ostreida (706)
- 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)
- Genus Tambanella Nakazawa & Newell, 1968 † (2)
- Genus Waagenoperna Tokuyama, 1959 † (3)
- Species Waagenoperna aurita J.-F. Xu, 1984 †
- Species Waagenoperna lateplanata (L. Waagen, 1907) †
- Species Waagenoperna sichuanensis J.-F. Xu, 1984 †
- 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 † (94)
- Order Pectinida (3 004)
- 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 (1 834)
- Class Conchifera accepted as Bivalvia
- Class Cricoconarida † (1)
- Class Gastropoda (102 753)
- 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