The Sea of Japan, a semi-enclosed sea in the North Pacific, is joined to neighboring waters via relatively narrow shallow straits. Accordingly, sea level regressions during the glacial periods likely resulted in the isolation of the Sea of Japan and the fragmentation of many populations of marine organisms. Based on molecular genetic analyses, I have revealed the impact of historical events for grand fish in the Sea of Japan. For example, clear genetic divergences between the Sea of Japan and other geographic regions of the North Pacific were found in the Sake-bikunin species of snailfish. The genetic divergence suggested that colder climates from the late Pliocene epoch and the isolation of the Sea of Japan during the Pleistocene epoch may have driven its divergence. Interestingly, similar patterns of genetic divergence have been detected in some other ground fish, which suggests that they have been isolated through a common historical event.