Marine environmental characteristics on the dinoflagellate cysts distribution in surface sediment of the southwest sea of Korea were investigated from 21 stations in September 2003, and 36 stations in June, 2004. The water mass characteristics indicated that the southwest sea of Korea is characterized by various oceanographic conditions due to coastal waters of Korea and China. The Tsushima warm currents and the cold bottom water of the Yellow Sea. Mud contents and chlorophyll a concentrations were higher in central region such as, Namhaedo, Yeosu and Goheung coast than in western region such as, Wando, Haenam and Jindo coast in the South Sea of Korea. A total of 35 taxa of dinoflagellate cysts were identified representing 21 genera, 33 species, 2 unidentified species. Cyst abundance ranged from 13 to 527 cysts $g-dry^{-1}$, showing higher abundance in the coastal areas than in western region of the South Sea of Korea. From the result of the PCA analysis, the distribution of dinoflagellate cysts was not only related to the different water masses which appeared in the southwestern sea but also to physical and biological parameters such as water temperature, light, surface sediment faces and phytoplankton biomass.