To assess short-term variation of summer phytoplankton community structure in different water masses, phytoplankton and environmental factors were monitored from 31 stations on and off the southern coasts of Korea, from June 18 to June 20 2009. According to multidimensional scaling (MDS) and cluster analysis based on phytoplankton community data from each station, the southern sea was divided into two groups. The first group included stations in the south-eastern region of Jeju Island, which is strongly influenced by the Kuroshio warm current. The second group located along the coastal region of the southern sea, which was mainly comprised of Bacillariophyceae and Crytophyceae. Of these stations, St. 13 and 28 formed a temperature front caused by different hydrological conditions. In particular, nutrients and Chl.a concentrations in these two stations were significantly higher compared to those in the other stations. This indicates that phytoplankton population and subsequent microalgal growth under high nutrient concentrations vary in different water masses. Our results support the theory that phytoplankton community structure in the southern sea of Korea can be influenced on a short-term scale by different water masses and currents.