The profile of a fixed site at station M ($34.77^{circ}N,;129.13^{circ}E$) in the Korea Strait was studied from March 2006 to February 2007. The aim was to understand the relationship between the annual thermal stratification pattern and seasonal variation in phytoplankton community structure. Physicochemical factors including temperature, salinity and nutrient concentrations, which strongly influence the proliferation and diversity of phytoplankton, were measured. The study period was divided into three due to the characteristic of thermohaline structures; mixed I (March-May 2006), stratified (June-November 2006) and mixed II(December 2006-Feburuary 2007). Diatoms dominated during the mixed I (89%) and II (48%) periods, while nanoplankton group occupied over 83% of total population during the stratified period. The dominant species during the mixed I and II was Chaetoceros socialis (47% and 29%, respectively), while during the stratified period Gyrodinium sp.(4%) was the most dominant. Averaged total chl a concentrations during the mixed I and II periods were 0.61 mg $m^{-3}$ and 0.72 mg $m^{-3}$, respectively, which were at least two-fold higher than that during the stratified period (0.30 mg $m^{-3}$). The vertical mixing and convection process of the water column induced nutrient supply from the bottom layer to the euphotic zone. It also led to the dominance of diatoms during the mixed periods, whereas small phytoplankton prevailed over large phytoplankton as stratification blocked the upward movement of nutrients to subsurface during the stratified period. During the mixed I and II periods, microplanktonic chl a dominated concentrations (50% and 48%, respectively), while picoplanktonic chl a occupied over 37% of total chl a during the stratified period.