We investigated the seasonal succession of phytoplankton assemblages in the eastern part of the South Sea of Korea in relation to surface water masses. The study areas are under the direct influence of the Tsushima Warm Current (TCW) throughout the whole year, with its strength known to be seasonally variable. The region is also influenced by coastal waters (CW) driven from the South Sea of Korea and East China Sea, particularly in summer, as indicated by low salinity in the surface water. Nutrient property of the TCW can reveals whether the origin of the TCW is the nutrient-rich Kuroshio Current or the oligotropic Taiwan Warm Current. Surface chlorophyll-a (Chl-a) concentrations displayed a large seasonal variation for all stations, with high values found in spring and autumn and low values in summer and winter. At station M (offshore) and P (intermediate location between M and R), Chl-a concentrations in October were higher than those in March, when spring bloom normally occurs. This may be related to deeper mixed layer depths in October. Diatoms dominated under conditions of high nutrient supply in which Chaetoceros spp. and Skeletonema costatum-like spp. were abundant. S. costatum-like spp. dominated at stations R (onshore station) and P in December when there was greater nutrient supply, especially of phosphate. Flagellates and dinoflagellates dominated at all three stations after diatoms blooms. Dominant species were Scrippsiella trochoid in April and Ceratium furca in October at station R, and Gyrodinium spp. and Gymnodinium spp. at station M during summer, when the effect of the oligotropic Taiwan Warm Current and the oligotropic coastal water from East China Sea were strong. Redundancy analysis showed clear seasonal successions in the phytoplankton community and environmental conditions, in which both principal components 1 and 2 accounted for 69.6% of total variance. Our results suggested that environmental conditions seemed to be determined by the origin of the TCW and the relative seasonal strength of the water masses of the TCW and CW, which may affect phytoplankton growth and compositions in the study area.