Short-term variations of phytoplankton community structure in the southeast coastal waters of Korea from July to September in 2006 were investigated with data set of phytoplankton, chemical and physical water properties, and meterological data. A total of 11 sampling sites of 4 different depths (surface, 5 m, 10 m, and bottom) were visited on July 11-14, July 24-26, August 7-10, August 21-24 and September 5-8. We identified 151 species in 63 genera of phytoplankton in which diatoms were the most diverse group composed of 92 species in 37 genera. Dinoflagellates were the second diverse group of 52 species in 22 genera. The other groups include 7 species in 4 genera including Raphidophytes, and Euglenophyta. After rainy season, excessive nutrients from adjacent streams to the stratified water column proliferates Chaetoceros group in July. But biomass of phytoplankton and nutrient concentrations were decreased during the period of a drought in August. However, Chaetoceros was the most dominant genera in all depths of the first, second, third and fifth cruises, except the 4th cruise on August 21-24 when dominant group were dinoflagellates including Gymnodinium spp. and Cochlodinium polykrikoides. The characteristic of phytoplankton community and environment condition during summer 2006 can be summarized as: 1) low concentration of nutrients caused by a long lasting drought in August 2) no summer outbreak of C. polykrikoides because the strength of offshore waters was weak than other years, and 3) Chaetoceros spp. was the dominant species despite short period appearance of dinoflagellates.