The Holocene history of the Japan Sea was reconstructed using foraminiferal assemblages and stable isotope records from two piston cores recovered from west of the Tsugaru Strait, with the overall goal to resolve a controversy regarding flow in and out of the Japan Sea during the Holocene. In the northern core the planktonic foraminifer N. pachyderma changed from left-coiling to right-coiling at 8.3 ka. However, in the southern core the left-coiling form remained dominant until 4.8 ka. Some indices of the stable isotopic records also changed at 8.3 and 4.8 ka. These results suggest that the Tsushima Current started to inflow into the Japan Sea at 8.3 ka, but a branch of the Oyashio Current continued to inflow until 4.8 ka. We attribute the coexistence of the two currents between 8.3 and 4.8 ka to the opposite direction flows between the shallow and the deep portions of the Tsugaru Strait driven by baroclinic components.