Phytoplankton community structure is one of the indicators that can explain the enviromnental characteristics of coastal waters. In this study, phytoplankton community structure and water quality of aquaculture area were investigated for understanding regional enviromnental characteristics. Thirty stations in aquaculture areas of Tongyeong, southeast coast of Korea, were investigated monthly from January to December, 2009. Phytoplankton community, meteorologic dada and enviromnent factors including temperature, salinity, transparency, nutrients and chlorophyll a were also examined. Chaetoceros spp. and unidentified small flagellates were dominant species in all the year round. Pseudo-nitzschia spp., Dictyocha spp., and Nitzschia longissima were dominant in June to October being summer season, and Skeletonema costatum, Thalassiosira spp., Eucamphia zodiacus, Akashiwo sanguinea, Gymnodinium spp. and Asterionella japonicus appeared as dominant species in the rest of months. Dinoflagellate blooms occurred 3 times in near Hansan Bay and around Saryang-do, and the highest chlorophyll a was found in Hansan Bay. Species diversity of phytoplankton was lower in Hansan and Womnum Bay, and diatom was more abundant than dinoflagellates in Mireuk-do waters. These results showed that phytoplankton community varied by the seasonal and geographical characteristics, and recent increase of water temperature and heavy rain may affect on phytoplankton community structure.