Between brackets is the number of accepted species

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- Mollusca (132 888)
- Subphylum Aculifera
- Subphylum Conchifera
- Subphylum Placophora accepted as Polyplacophora
- Superclass Aplacophora
- Class Amphineura accepted as Aculifera
- Class Bivalvia (25 022)
- Subclass Autobranchia (23 308)
- Infraclass Heteroconchia (16 648)
- Infraclass Pteriomorphia (6 660)
- Superorder Eupteriomorphia
- Order Arcida (1 227)
- Order Colpomyida † (6)
- Order Cyrtodontida † (66)
- Order Limida (358)
- Order Myalinida † (576)
- Superfamily Alatoconchoidea H. Termier, G. Termier & de Lapparent, 1974 †
- Superfamily Ambonychioidea S. A. Miller, 1877 † (71)
- Superfamily Prokopievskioidea H. E. Vokes, 1967 † (505)
- Family Anadontellidae Silantiev, 2011 † (34)
- Family Anthraconautidae Kanev, 1980 † accepted as Naiaditidae Scarlato & Starobogatov, 1979 †
- Family Kinerkaellidae Scarlato & Starobogatov, 1979 † accepted as Kinerkaellinae Scarlato & Starobogatov, 1979 †
- Family Naiaditidae Scarlato & Starobogatov, 1979 † (291)
- Family Prokopievskiidae H. E. Vokes, 1967 † (180)
- Subfamily Abiellinae Starobogatov, 1970 † (29)
- Subfamily Concinellinae Silantiev, 2011 † (37)
- Subfamily Kinerkaellinae Scarlato & Starobogatov, 1979 † (75)
- Subfamily Prokopievskiinae H. E. Vokes, 1967 † (39)
- Genus Amnigeniella Betekhtina, 1966 † (5)
- Genus Brussiella Betekhtina, 1966 † (3)
- Genus Dictys Khalfin, 1950 † (1)
- Genus Gangamya Silantiev & Chandra, 2015 † (3)
- Genus Junjagiana Jatsuk, 1979 † (2)
- Genus Kemeroviella Betekhtina, 1974 † (4)
- Genus Procopievskia Ragozin, 1933 † accepted as Prokopievskia Khalfin, 1950 †
- Genus Prokopievskia Khalfin, 1950 † (14)
- Genus Raniganjelia Silantiev & Chandra, 2015 † (1)
- Genus Sinomya Pogorevich, 1977 † (5)
- Genus Zvonarevia Tokareva, 1988 † (1)
- Genus Iniana Ragozin, 1961 †
- Genus Iniella Ragozin, 1956 †
- Genus Kemerovskia Ragozin, 1956 †
- Genus Kusbassoconcha Ragozin, 1956 †
- Family Sinomyidae Scarlato & Starobogatov, 1979 † accepted as Prokopievskiidae H. E. Vokes, 1967 †
- Order Mytilida (707)
- Order Ostreida (706)
- 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 (1 838)
- Class Conchifera accepted as Bivalvia
- Class Cricoconarida † (1)
- Class Gastropoda (102 777)
- 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