Glacial-interglacial sea level changes have caused drastic variations in the surface hydrography, ventilation and ecosystem structure in the Japan Sea. Previous reconstructions using microfossils and geochemical proxies suggested decreased productivity and a more calcareous plankton community during glacial periods. However, the inferred community structure change is not consistent with significantly lower salinity in the Japan Sea during the glacials, which would have had a deleterious effect on calcareous plankton growth. Here, biomarker records of ODP Site 797 are generated to further evaluate phytoplankton productivity and community structure changes in the Japan Sea over the last 166 kyr. Although the contents of the phytoplankton biomarkers changed by two to three orders of magnitude, there were no clear glacial-interglacial patterns as sediment biomarker contents reflected the combined effect of production and water column degradation. The collective assessments of our biomarker records and published records support previous conclusions of decreased productivity in the Japan Sea during the glacials. However, a community structure proxy based on the alkenone/brassicasterol ratio reveals a shift from a diatom-dominated community during the glacials to a coccolithophorid-dominated community during the interglacials, mainly as a result of surface salinity variations in the Japan Sea controlled by sea-level changes. Previous community structure reconstruction using biogenic carbonate/silica ratio could have been complicated by the different environmental factors governing silica and CaCO (sub 3) dissolution in the Japan Sea. Abstract Copyright (2011) Elsevier, B.V.