The soft-shell clam Mya arenaria Linnaeus, 1758 is a commercially important fishery resource that occurs in boreal and temperate environments in the Northern Hemisphere. Whether the soft-shell clam is a single species with a circumboreal range or a species complex also comprising Mya japonica Jay, 1857 distributed in the north Pacific has long been debated by malacologists and palaeontologists based on slight differences in shell morphology. We used an integrative taxonomic approach incorporating available Mya spp. mitochondrial COI and 16S rRNA, and nuclear 28S rRNA gene sequences, as well as spermatozoan and shell morphological characters to test the validity of M. japonica and examine the range of soft-shell clam distribution. Although differences in shell morphology were minor, the results from tree topologies, pairwise uncorrected p-distances, Automatic Barcode Gap Discovery (ABGD) and spermatozoan ultramorphological data confirm the validity of M. japonica in both its endemic region in the northwest Pacific, and as here newly reported introduced populations in British Columbia in the northeast Pacific, and show that M. arenaria is distributed in the northeast Pacific, North Atlantic, Barents Sea (Arctic Ocean) and Mediterranean. We estimate these two closely related sister species diverged 4.1–12.5 Myr during early Pliocene to late Miocene, which is consistent with current evolutionary theory regarding M. arenaria. In addition, ABGD indicated the congener Mya truncata Linnaeus, 1758 may represent a species complex, but additional evidence is still needed to clarify its taxonomic status.