The fossil record of extant vesicomyid bivalve species from Japan is re-evaluated, based on newly collected material and a literature survey. Calyptogena pacifica Dall was newly collected from the upper Miocene Akaishi Formation in Aomori Prefecture. The new data support previous observations that the extant C. pacifica has been distributed along the Japan Sea borderland since the late Miocene, although it is not living in the Japan Sea today. It is shown that the shell described by Yokoyama (1925) from the Pliocene Hitachi Formation in Ibaraki Prefecture as Tapes undulatus (Born) is another Recent species, Archivesica kawamurai (Kuroda). On the other hand, it is clear that Akebiconcha cf. kawamurai illustrated by Katto & Masuda (1978) from the lower Miocene Shikiya Formation in Wakayama Prefecture is not Archivesica kawamurai. In contrast to C. pacifica, A. kawamurai appeared in the Pliocene and was distributed along the Pacific side of southwestern and central Japan, where the species is still living today. Consequently, among sixteen Recent species of Pliocardiinae, only two have a fossil record.