We investigated short-term variations of phytoplankton community structure according to marine environmental condition with data set of phytoplankton composition, nutrients, physical parameters and precipitation. The 13 sampling stations were located in the southeast coastal waters of Korea, the survey monthly carried out from March to November. The study area can be divided into two zone according to the characteristics of marine environment. Zone I is the occupied with Thalassiosira decipiens, Skeletonema costatum, Eucampia zodiacus, Cheatoceros spp. and Asterionellopsis glacialis due to continuous freshwater input and high concentration of nutrients. Zone II was dominated by Pseudo-nitzschia spp. probably due to rainfall and self eutrophication of aquaculture farm.