This study was to determine the fluctuation in phytoplankton assemblages with regarding to environmental conditions and nutrients, which were surveyed around Mokpo waters in the southwestern waters, Korea. Sampling was carried out on the Mokpo, Sinan, and Wando coasts from March to November 2003. The maximum sea surface temperature was recorded in August, and it ranged around $25^{\circ}C$ regardless of sampling sites. However, salinity in Mokpo waters showed a great variation, which ranged from 5-30 psu and recoded the minimum of 5 psu in July and the maximum of 30 psu in November. Moreover, in Mokpo waters, the chlorophyll a and SS concentration of the surface layer were also the highest values of $20\;{\mu}g\;l^{-1}\;and\;40\;{\mu}g\;l^{-1}$, respectively than those of Sinan and Wando waters. The concentrations of $NH_4-N,\;NO_2-N,\;NO_3-N,\;and\;PO_4-P$ were also he highest values of $0.018\;{\mu}mol\;^l{-1},\;0.062\;{\mu}mol\;l^{-1},\;1.2\;{\mu}mol\;l^{-1}\;and\;0.078\;{\mu}mol\;l^{-1}$, respectively in Morpo waters than those of Sinan and Wando waters. During the period of this study, the majority of the taxa were diatoms; Thalassiosira rotula, Rhizosolenia setigera, Prorocentrum minimum, Chaetoceros curvisetus, Leptocylindrus danicus, Pseudonitzschia pungens, and Chaetoceros spp. were detected in the dominant species of phytoplankton. The dinoflagellates were relatively abundant during the summer season in Wando waters, which attained an abundance of $10-20\%$. In Mokpo waters, DIN/DIP was the highest value of 700 in March, whereas the lowest was shown in Wando waters. However, DIN/DIP value in summer at Wando waters was extremely reversed, which appeared to be associated with the development of dinoflagellates. On the bais of factor analysis using SYSAT 6.0, nutrient showed somewhat correlation with chlorophyll a. Consequently, the process of discharge of fresh water in Mokpo waters plays an important role in extremely fluctuation in nutrients and conditions. Although Wando waters maintains a lack of nutrients, it should be influenced by different water current and may be associated with a concentration of nutrients.