In order to characterize the distribution and community structure of phytoplankton, chlorophyll and carotenoid pigments, nutrients, and hydrographic variables were measured in the coastal waters off Jeju Island, Korea, during 11-13 May 2005. The photosynthetic pigments were analyzed using a highperformance liquid chromatograph (HPLC), and were used to calculate the algal class abundances using the CHEMTAX program. There was a distinct difference in phytoplankton abundance and community composition between the northern coastal water (NCW) and the southern coastal water (SCW) of this island. The chlorophyll a concentrations were $sim$26% higher in NCW than in SCW. Diatoms were predominant (> 50%) in NCW, while the phytoplankton composition was more diverse in SCW. Considering the hydrographic conditions and nutrient distributions in the study region, the sharp structural change in phytoplankton community seems to be mainly due to the slight difference in the origin of NCW and SCW. This study shows that HPLC-pigment measurements are useful for identifying sharp structural changes in phytoplankton communities in dynamic coastal environments.