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)
- Family Arctostreidae Vialov, 1983 † (2)
- Family Chondrodontidae Freneix, 1960 †
- Family Crassostreidae Scarlato & Starobogatov, 1979 accepted as Crassostreinae Scarlato & Starobogatov, 1979
- Family Eligmidae Gill, 1871 † (1)
- Family Flemingostreidae Stenzel, 1971 (12)
- Family Gryphaeidae Vialov, 1936 (62)
- Subfamily Exogyrinae Vialov, 1936 † (14)
- Subfamily Gryphaeinae Vialov, 1936 † (11)
- Tribe Gryphaeini Vialov, 1936 † (10)
- Genus Gryphaea Lamarck, 1801 † (10)
- Subgenus Gryphaea (Africogryphaea) Freneix, 1965 † represented as Gryphaea Lamarck, 1801 †
- Subgenus Gryphaea (Bilobissa) Stenzel, 1971 † represented as Gryphaea Lamarck, 1801 †
- Subgenus Gryphaea (Gryphaea) Lamarck, 1801 † represented as Gryphaea Lamarck, 1801 †
- Subgenus Gryphaea (Notostrea) H. J. Finlay, 1928 accepted as Pycnodonte Fischer von Waldheim, 1835
- Subgenus Gryphaea (Odontogryphaea) Ihering, 1903 †
- Species Gryphaea angulata Lamarck, 1819 accepted as Crassostrea angulata (Lamarck, 1819)
- Species Gryphaea angulata Lamarck, 1801 accepted as Crassostrea angulata (Lamarck, 1819)
- Species Gryphaea aquila Brongniart, 1822 † accepted as Aetostreon latissimum (Lamarck, 1801) †
- Species Gryphaea arcta K. F. Braun, 1841 † accepted as Mesogena arcta (K. F. Braun, 1841) †
- Species Gryphaea arcuata Lamarck, 1801 †
- Species Gryphaea arcuataeformis Kiparisova, 1936 †
- Species Gryphaea athyroides Guppy, 1866 †
- Species Gryphaea avicularis Münster, 1841 †
- Species Gryphaea bilobata J. De C. Sowerby, 1840 †
- Species Gryphaea buchsii Grewingk, 1853 † accepted as Sokolowia buchsii (Grewingk, 1853) †
- Species Gryphaea bullata J. Sowerby, 1822 †
- Species Gryphaea calceola Quenstedt, 1843 †
- Species Gryphaea chakii McLearn, 1937 † accepted as Gryphaea arcuataeformis Kiparisova, 1936 †
- Species Gryphaea cochlear (Poli, 1795) accepted as Neopycnodonte cochlear (Poli, 1795)
- Species Gryphaea columba Lamarck, 1819 † accepted as Rhynchostreon suborbiculatum (Lamarck, 1801) †
- Species Gryphaea concors Ihering, 1902 †
- Species Gryphaea controversa Roemer, 1835 †
- Species Gryphaea costellata (Douvillé, 1916) †
- Species Gryphaea couloni Defrance, 1821 † accepted as Aetostreon latissimum (Lamarck, 1801) †
- Species Gryphaea cuccullata (Born, 1778) accepted as Saccostrea cuccullata (Born, 1778)
- Species Gryphaea cymbiola Deshayes, 1832 † accepted as Pycnodonte cymbiola (Deshayes, 1832) †
- Species Gryphaea defrancii Deshayes, 1832 † accepted as Pycnodonte defrancii (Deshayes, 1832) †
- Species Gryphaea dilatata J. Sowerby, 1816 †
- Species Gryphaea esterhazyi Pavay, 1871 † accepted as Sokolowia buchsii (Grewingk, 1853) †
- Species Gryphaea eversa Melleville, 1843 † accepted as Gryphaeostrea eversa (Melleville, 1843) †
- Species Gryphaea gasar (Dautzenberg, 1891) accepted as Crassostrea tulipa (Lamarck, 1819)
- Species Gryphaea gigantea J. De C. Sowerby, 1823 †
- Species Gryphaea gryphoides (Schlotheim, 1813) † accepted as Crassostrea gryphoides (Schlotheim, 1813) †
- Species Gryphaea keilhaui J. Böhm, 1904 †
- Species Gryphaea laeviuscula Zieten, 1833 †
- Species Gryphaea latissima Lamarck, 1801 † accepted as Aetostreon latissimum (Lamarck, 1801) †
- Species Gryphaea maccullochii J. De C. Sowerby, 1827 †
- Species Gryphaea minuta J. De C. Sowerby, 1827 †
- Species Gryphaea minuta Feldtmann, 1963 †
- Species Gryphaea miradorensis C. S. Petersen, 1946 †
- Species Gryphaea nana J. Sowerby, 1822 † accepted as Nanogyra nana (J. Sowerby, 1822) †
- Species Gryphaea navicula Monterosato, 1884 accepted as Neopycnodonte cochlear (Poli, 1795)
- Species Gryphaea nevadensis McRoberts, 1992 †
- Species Gryphaea obliquata J. Sowerby, 1815 †
- Species Gryphaea ovalis Zieten, 1833 †
- Species Gryphaea pharaonum P. Oppenheim, 1903 †
- Species Gryphaea plicifera Dujardin, 1837 † accepted as Ceratostreon pliciferum (Dujardin, 1837) †
- Species Gryphaea polymorpha Münster, 1833 †
- Species Gryphaea praecochlear P. Oppenheim, 1903 †
- Species Gryphaea pseudovesicularis Gümbel, 1861 † accepted as Pycnodonte pseudovesicularis (Gümbel, 1861) †
- Species Gryphaea rocana Ihering, 1903 †
- Species Gryphaea rostrigera Ihering, 1902 †
- Species Gryphaea sewerzowii Romanowsky, 1884 † accepted as Ferganea sewerzowii (Romanovsky, 1884) †
- Species Gryphaea sinuata J. Sowerby, 1822 † accepted as Aetostreon latissimum (Lamarck, 1801) †
- Species Gryphaea skuld J. Böhm, 1904 † accepted as Gryphaea keilhaui J. Böhm, 1904 †
- Species Gryphaea suborbiculata Lamarck, 1801 † accepted as Rhynchostreon suborbiculatum (Lamarck, 1801) †
- Species Gryphaea tarda F. W. Hutton, 1873 † accepted as Pycnodonte tarda (F. W. Hutton, 1873) †
- Species Gryphaea teicherti Feldtmann, 1963 †
- Species Gryphaea trachyoptera C. A. White, 1887 †
- Species Gryphaea virleti (Deshayes, 1835) † accepted as Saccostrea virleti (Deshayes, 1835) †
- Species Gryphaea weberae Yanin, 1969 † accepted as Pycnogryphaea weberae (Yanin, 1969) †
- Genus Gryphites Schlotheim, 1813 † accepted as Gryphaea Lamarck, 1801 †
- Genus Liogryphaea P. Fischer, 1886 † accepted as Gryphaea Lamarck, 1801 †
- Tribe Pernostreini Kosenko, 2017 †
- Genus Catinula Rollier, 1911 † (1)
- Subfamily Pycnodonteinae Stenzel, 1959 (37)
- Genus Gigantostrea Sacco, 1897 † accepted as Pycnodonte Fischer von Waldheim, 1835
- Family Ostreidae Rafinesque, 1815 (166)
- 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)
- 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