• Calyptogena Dall, 1891
• Calyptogena (Abyssogena) Krylova, Sahling & R. Janssen, 2010 accepted as Abyssogena Krylova, Sahling & R. Janssen, 2010
• Calyptogena (Abyssogena) mariana Okutani, Fujikura, H. Watanabe & Ohara, 2013 accepted as Abyssogena mariana (Okutani, Fujikura, H. Watanabe & Ohara, 2013)
• Calyptogena (Archivesica) Dall, 1908 accepted as Archivesica Dall, 1908
• Calyptogena (Archivesica) edisonensis Okutani, Kojima & Kim, 2004 accepted as Phreagena edisonensis (Okutani, Kojima & D. Kim, 2004)
• Calyptogena (Archivesica) fortunata Okutani, Kojima, Kawato, Seo & Fujikura, 2011 represented as Calyptogena fortunata Okutani, Kojima, Kawato, Seo & Fujikura, 2011
• Calyptogena (Archivesica) garuda Okutani & Soh, 2005 accepted as Archivesica garuda (Okutani & Soh, 2005)
• Calyptogena (Archivesica) kilmeri F. R. Bernard, 1974 accepted as Phreagena kilmeri (F. R. Bernard, 1974)
• Calyptogena (Archivesica) magnocultellus Okutani, Kojima & Iwasaki, 2002 accepted as Archivesica magnocultellus (Okutani, Kojima & Iwasaki, 2002)
• Calyptogena (Archivesica) tsubasa Okutani, Fujikura & Kojima, 2000 accepted as Archivesica tsubasa (Okutani, Fujikura & Kojima, 2000)
• Calyptogena (Ectenagena) Woodring, 1938 accepted as Ectenagena Woodring, 1938
• Calyptogena (Ectenagena) australis Stuardo & Valdovinos, 1988 accepted as Ectenagena australis (Stuardo & Valdovinos, 1988)
• Calyptogena (Ectenagena) fossajaponica Okutani, Fujikura & Kojima, 2000 accepted as Isorropodon fossajaponicum (Okutani, Fujikura & Kojima, 2000)
• Calyptogena (Ectenagena) kaikoi Okutani & Métivier, 1986 accepted as Abyssogena kaikoi (Okutani & Métivier, 1986)
• Calyptogena (Ectenagena) laubieri Okutani & Métivier, 1986 accepted as Ectenagena laubieri (Okutani & Métivier, 1986)
• Calyptogena (Ectenagena) laubieri kurilensis Okutani & Kato, 2009 represented as Ectenagena laubieri kurilensis (Okutani & Kato, 2009)
• Calyptogena (Ectenagena) laubieri laubieri Okutani & Métivier, 1986 accepted as Ectenagena laubieri laubieri (Okutani & Métivier, 1986)
• Calyptogena (Ectenagena) magnifica Boss & R. D. Turner, 1980 accepted as Turneroconcha magnifica (Boss & R. D. Turner, 1980)
• Calyptogena (Ectenagena) nautilei Okutani & Métivier, 1986 accepted as Ectenagena nautilei (Okutani & Métivier, 1986)
• Calyptogena (Ectenagena) phaseoliformis Métivier, Okutani & Ohta, 1986 accepted as Abyssogena phaseoliformis (Métivier, Okutani & Ohta, 1986)
• Calyptogena akanudaensis Tanaka, 1959 † accepted as Adulomya akanudaensis (Tanaka, 1959) † accepted as Pleurophopsis akanudaensis (Tanaka, 1959) †
• Calyptogena birmani Domaneschi & Lopes, 1990 accepted as Callogonia venusta (Dall, 1886) accepted as Vesicomya venusta (Dall, 1886)
• Calyptogena bosoensis Kanie & Kuramochi, 2001 † accepted as Archivesica bosoensis (Kanie & Kuramochi, 2001) †
• Calyptogena chinookensis Squires & Goedert, 1991 † accepted as Pleurophopsis chinookensis (Squires & Goedert, 1991) †
• Calyptogena costaricana Krylova & Sahling, 2006
• Calyptogena diagonalis Barry & Kochevar, 1999
• Calyptogena elongata Dall, 1916 accepted as Ectenagena elongata (Dall, 1916)
• Calyptogena extenta (Krylova & Moskalev, 1996)
• Calyptogena fausta Okutani, Fujikura & Hashimoto, 1993
• Calyptogena fortunata Okutani, Kojima, Kawato, Seo & Fujikura, 2011
• Calyptogena fossajaponica Okutani, Fujikura & Kojima, 2000 accepted as Isorropodon fossajaponicum (Okutani, Fujikura & Kojima, 2000)
• Calyptogena gallardoi Sellanes & Krylova, 2005
• Calyptogena gigas (Dall, 1896) accepted as Archivesica gigas (Dall, 1896)
• Calyptogena goffrediae Krylova & Sahling, 2006
• Calyptogena kawamurai (Kuroda, 1943) accepted as Akebiconcha kawamurai Kuroda, 1943 accepted as Archivesica kawamurai (Kuroda, 1943)
• Calyptogena laubieri Okutani & Métivier, 1986 accepted as Ectenagena laubieri (Okutani & Métivier, 1986)
• Calyptogena laubieri kurilensis Okutani & Kato, 2009 accepted as Ectenagena laubieri kurilensis (Okutani & Kato, 2009)
• Calyptogena lepta (Dall, 1896) accepted as Wareniconcha lepta (Dall, 1896)
• Calyptogena magnifica Boss & R. D. Turner, 1980 accepted as Turneroconcha magnifica (Boss & R. D. Turner, 1980)
• Calyptogena makranensis Krylova & Sahling, 2006
• Calyptogena marissinica C. Chen, Okutani, Q. Liang & J.-W. Qiu, 2018
• Calyptogena nankaiensis Okutani, Kojima & Ashi, 1996 accepted as Phreagena nankaiensis (Okutani, Kojima & Ashi, 1996)
• Calyptogena nanshaensis F.-S. Xu & S.-P. Shen, 1991 accepted as Laubiericoncha nanshaensis (F.-S. Xu & S.-P. Shen, 1991) accepted as Archivesica nanshaensis (F.-S. Xu & S.-P. Shen, 1991)
• Calyptogena nautilei Okutani & Métivier, 1986 accepted as Ectenagena nautilei (Okutani & Métivier, 1986)
• Calyptogena nipponica Oinomikado & Kanehara, 1938 † accepted as Archivesica nipponica (Oinomikado & Kanehara, 1938) †
• Calyptogena okutanii Kojima & Ohta, 1997 accepted as Phreagena okutanii (Kojima & Ohta, 1997)
• Calyptogena pacifica Dall, 1891
• Calyptogena packardana Barry, Kochevar, Baxter & Harrold, 1997
• Calyptogena ponderosa Boss, 1968 accepted as Pliocardia ponderosa (Boss, 1968)
• Calyptogena rectimargo Scarlato, 1981
• Calyptogena regab Cosel & Olu, 2009 accepted as Christineconcha regab (Cosel & Olu, 2009)
• Calyptogena shiretokensis S. Uozumi, 1967 † accepted as Archivesica shiretokensis (S. Uozumi, 1967) †
• Calyptogena similaris Okutani, Kojima & Ashi, 1997 accepted as Archivesica similaris (Okutani, Kojima & Ashi, 1997)
• Calyptogena solidissima Okutani, Hashimoto & Fujikura, 1992 accepted as Archivesica kawamurai (Kuroda, 1943)
• Calyptogena soyoae Okutani, 1957 accepted as Phreagena soyoae (Okutani, 1957)
• Calyptogena starobogatovi Krylova & Sahling, 2006
• Calyptogena tuerkayi Krylova & R. Janssen, 2006
• Calyptogena valdiviae (Jaeckel & Thiele, 1931)
• Calyptogena veneriformis Amano & Kiel, 2012 †