Paleoceanographic changes in the East/Japan Sea during the late Quaternary based on high-resolution elemental variations, particularly correlations between dark–light laminations and millennial-scale climatic changes, have remained poorly understood because of the lack of the high-resolution proxies. The recent application of micro-X-ray fluorescence (XRF) core scanning provides the potential for high-resolution study on the laminations deposited in the East/Japan Sea. In this study, we present a geochemical study by using micro-XRF core scanning on a 730 cm core recovered from the East/Japan Sea. Elemental variations and factor analysis indicate that the sedimentary environment changed from anoxic to suboxic conditions from Marine Isotope Stage (MIS) 2–3 to MIS 1, which is induced by increased contribution of high-salinity sea water from the open ocean due to the rising sea level. The dark and light laminations during MIS 2–3 were correlated with Dansgaard–Oeschger cycles and summer monsoon proxy, with dark-colored sediments related to higher terrigenous concentration, corresponding to warm–moist and enhanced summer monsoon period. During the interstadial period, more terrigenous sediments were transported to the East/Japan Sea via the strengthened fluvial discharge from the surrounding continents, caused by enhanced monsoon rainfall. Thus the development of the East Asian summer monsoon and consequent variations in fluvial discharge would have significantly affected the paleoceanographic conditions in the East/Japan Sea during the MIS 2–3 sea-level lowstand. Copyright © 2012 John Wiley & Sons, Ltd.