No previous studies have investigated changes in the offshore molluscan assemblages of the Japan Sea during the last deglacial period. We examined the sedimentary facies and the stratigraphic distribution of molluscs in cored sediments collected at 132 m water depth off Sado Island, Japan. The ages of 13 specimens of molluscan shells were determined by ¹⁴C dating. Moreover, we analyzed the relative abundance of the planktonic foraminifer Globigerinoides ruber, which is a proxy of the Tsushima Current. The results show that the cored sediments were deposited from 13,574 ± 121 cal yr BP at a water depth that increased over time from about 50 m to 132 m. Three sedimentary facies are recognized in the cored sediment, in ascending stratigraphic order; coquina sediments, massive silt, and massive fine sand yielding many molluscan shells. The change in substrate was caused mainly by variability in the input of terrigenous deposits at 10,640–9,300 cal yr BP (the transition from coquina to silt) and at 8,860–5,180 cal yr BP (the transition from silt to sand).¹⁴C data show that the molluscan species Porterius dalli, Cyclocardia ferruginea, Tridonta alaskensis and Puncturella nobilis were living in the Japan Sea before the initial inflow of the Tsushima Current at 9,300 cal yr BP. The modern molluscan fauna in the study area, which is dominated by Limopsis belcheri and Crenulilimopsis oblonga, may have become established by at least 5,180 cal yr BP.