Major changes occurred in the benthic molluscan fauna of the Sea of Japan continental shelf during the transition from Pleistocene glacial to interglacial stages, owing to rapid warming associated with the inflow of the warm Tsushima Current. Molluscan associations representing this transition occur in the lower Pleistocene Omma Formation in central Japan and suggest that there were two patterns of faunal change. The first was when warm-water species migrated into the Sea of Japan and lived along with cold-water species, accompanied by a northward shift in species ranges. The second pattern involved the migration of warm-water mollusks shortly after the local extinction of cold-water species. In the latter, it is possible that benthic molluscan communities with very low diversity and density existed temporarily and locally at inner shelf depths (<100 m) during the warming phase. Such a community has no modern analogue, but may have resulted from a marine climate with a higher seasonality than occurs today. These findings show that episodes of rapid warming have severe impacts on offshore benthic communities and molluscan species that include patterns not represented by modern faunal distributions.