Photosynthetic pigments, nutrients, and hydrographic variables were examined in order to elucidate the spatio-temporal variation of water column structure and its effect on phytoplankton community structure in the western channel of the Korea Strait in fall 2006 and spring 2007. High phytoplankton biomass in the spring was associated with high salinity, implying that nutrients were not supplied by coastal waters or the Yangtze-River Diluted water (YRDW) with low salinity. Expansion of the Korea Strait Bottom Cold Water (KSBCW) and a cold eddy observed during the spring season might enhance the nutrient supply from the subsurface layer to the euphotic zone. Chemotaxonomic examination showed that diatoms accounted for 60-70% of total biomass, followed by dinoflagellates. Nutrient supply by physical phenomena such as the expansion of the KSBCW and the occurrence of a cold eddy appears to be the controlling factors of phytoplankton community composition in the Korea Strait. Further study is needed to elucidate the mechanisms by which the KSBCW is expanded, and its role in phytoplankton dynamics.