We surveyed 23 sites of Jinhae Bay in spring and summer 2010 in order to study the correlation between the variation of environmental factors, including salinity, temperature, and nutrients and the characteristics of phytoplankton community structures in summer stratification. Phytoplankton biomass was high in the surface water in summer; however, it was very low in the bottom water. The results showed a negative correlation between chlorophyll a (chl. a) and nutrients (silicate, nitrate, nitrite, ammonium, and phosphate) or nutrients ratio in summer; however, there was mostly a positive correlation between chl. a and these nutrients in spring. This inconsistent correlation between spring and summer was attributed to the phytoplankton community, because a diverse phytoplankton community has different nutrient uptake abilities. In addition, the results of CCA (canonical correspondence analysis) showed a negative correlation between phosphate and dominant species, including Chaetoceros spp., Skeletonema costatum-like spp., and Pseudo-nitzschia delicatissima in summer, but a strong positive correlation between DIN (dissolved inorganic nitrogen) and the dominant species, including Cryptomonas spp. and Pseudo-nitzschia multistriata in spring. Consistently, the dominant algal species in summer showed a relatively smaller size cells compared with those in spring, suggested that it may have related with the low nutrient levels at surface layer due to strong stratified water column of summer.