Pliocene strata (4–3 Ma) in the Togakushi area, central Japan, yield significant ostracods, which allow investigation of the origins of high-latitude (Arctic–Atlantic) taxa and the Japan Sea endemic species, together with their post-Miocene history of extinction-speciation and migration. Three types of extinct species are found here: (1) cryophilic species in common with, or closely related to, species in Plio-Pleistocene assemblages described from the Japan Sea; (2) species closely related to, or comparable with, species that characterize Miocene Japan; and (3) species endemic to the Pliocene Japan Sea. Type (1) contains species closely related to high-latitude species known from the Arctic and northern Atlantic Oceans. Their presence suggests migration from the northwestern Pacific to the northern Atlantic through the Arctic seas since the Late Pliocene after the opening of the Bering Strait. Both Types (2) and (3) contain genera originating in the south, which show high specific diversity in regions affected by the modern warm Kuroshio Current. Ancestral ostracods of Types (2) and (3) invaded the Japan Sea from the Pacific from the Middle Miocene, and diversified to produce closely related species in the semi land-locked Japan Sea until the Early Pliocene. Two new species Aurila togakushiensis sp. nov. and Aurila shigaramiensis sp. nov. are described.