Many micropaleontological studies based on data from on-land sections, oil wells, and deep-sea drilling cores have provided important information about environmental changes in the Japan Sea that are related to the global climate and the local tectonics of the Japanese Islands. Here, major changes in the microfossil assemblages during the Late Pliocene to Early Pleistocene are reviewed. Late Pliocene (3.5-2.7 Ma) surface-water assemblages were characterized mainly by cold-temperate planktonic flora and fauna (nannofossils, diatoms, radiolarians, and planktonic foraminifera), suggesting that nutrient-rich North Pacific surface waters entered the Japan Sea via northern straits. The common occurrence of Pacific-type deep-water radiolarians during this period also suggests that deep water from the North Pacific entered the Japan Sea via the northern straits, indicating a sill depth >500 m. A weak warm-water influence is recognized along the Japanese coast, suggesting a small inflow of warm water via a southern strait. Nannofossil and sublittoral ostracod assemblages record an abrupt cooling event at 2.75 Ma that correlates with the onset of the Northern Hemisphere glaciation. Subsequently, cold intermediate-and deep-water assemblages of ostracods and radiolarians increased in abundance, suggesting active ventilation and the formation of the Japan Sea Proper Water, associated with a strengthened winter monsoon. Pacific-type deep-water radiolarians also disappeared around 2.75 Ma, which is attributed to the intermittent occurrence of deep anoxic environments and limited migration from the North Pacific, resulting from the near-closure or shallowing of the northern strait by a eustatic fall in sea level and tectonic uplift of northeastern Japan. A notable reduction in primary productivity from 2.3 to 1.3 Ma also suggests that the nutrient supply from the North Pacific was restricted by the near-closure of the northern strait. An increase in the abundance of subtropical surface fauna suggests that the inflow of the Tsushima Warm Current into the Japan Sea via a southern strait began at 1.7 Ma. The opening of the southern strait may have occurred after the subsidence of southwestern Japan.