Between brackets is the number of accepted species

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- Mollusca (132 791)
- Subphylum Aculifera
- Subphylum Conchifera
- Subphylum Placophora accepted as Polyplacophora
- Superclass Aplacophora
- Class Amphineura accepted as Aculifera
- Class Bivalvia (25 009)
- Subclass Autobranchia (23 295)
- Infraclass Heteroconchia (16 637)
- Infraclass Pteriomorphia (6 658)
- Superorder Eupteriomorphia
- Order Arcida (1 227)
- Order Colpomyida † (6)
- Order Cyrtodontida † (66)
- Order Limida (358)
- Order Myalinida † (576)
- Order Mytilida (706)
- Order Ostreida (705)
- Order Pectinida (3 004)
- Superfamily Anomiacea accepted as Anomioidea Rafinesque, 1815
- Superfamily Anomioidea Rafinesque, 1815 (73)
- Superfamily Aviculopectinoidea Meek & Hayden, 1865 † (98)
- Superfamily Buchioidea L. R. Cox, 1953 † (86)
- Superfamily Chaenocardioidea S. A. Miller, 1889 † (20)
- Superfamily Dimyoidea P. Fischer, 1886 (42)
- Superfamily Entolioidea Teppner, 1922 † (106)
- Superfamily Euchondrioidea Newell, 1938 † (14)
- Superfamily Eurydesmatoidea Reed, 1932 † (2)
- Superfamily Heteropectinoidea Beurlen, 1954 † (92)
- Family Acanthopectinidae Newell & Boyd, 1995 † accepted as Acanthopectininae Newell & Boyd, 1995 †
- Family Annuliconchidae Astafieva, 1995 † (2)
- Family Antijaniridae Hautmann, 2011 † (20)
- Family Asoellidae Begg & H. J. Campbell, 1986 † accepted as Asoellinae Begg & H. J. Campbell, 1986 † (1)
- Family Cassianoididae Newell & Boyd, 1995 † accepted as Cassianoidinae Newell & Boyd, 1995 †
- Family Heteropectinidae Beurlen, 1954 † (27)
- Subfamily Cassianoidinae Newell & Boyd, 1995 † (2)
- Subfamily Etheripectininae Waterhouse, 1982 † (11)
- Genus Etheripecten Waterhouse, 1963 † (8)
- Genus Fletcheripecten Waterhouse, 1982 † (3)
- Subfamily Girtypectininae Waterhouse, 2008 † (4)
- Subfamily Heteropectininae Beurlen, 1954 † (7)
- Genus Neomorphotis H.-F. Yin & J.-R. Yin, 1983 † (2)
- Genus Vnigripecten Muromzeva, 1984 † (1)
- Family Hunanopectinidae H.-F. Yin, 1985 † (8)
- Family Limipectinidae Newell & Boyd, 1990 † (17)
- Family Ornithopectinidae Hautmann, 2011 † (17)
- Superfamily Leiopectinoidea Krasilova, 1959 † (7)
- Superfamily Oxytomoidea Ichikawa, 1958 † (20)
- Superfamily Pectinacea accepted as Pectinoidea Rafinesque, 1815
- Superfamily Pectinoidea Rafinesque, 1815 (2 301)
- Superfamily Plicatuloidea Gray, 1854 (56)
- Superfamily Prospondyloidea Pchelintseva, 1960 † (13)
- Superfamily Pseudomonotoidea Newell, 1938 † (2)
- Superfamily Pterinopectinoidea Newell, 1938 † (72)
- Family Pernopectinoidea Newell, 1938 accepted as Entolioidea Teppner, 1922 †
- Family Saharopteriidae G. Termier & H. Termier, 1972 †
- 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 (102 697)
- 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