The seasonal variations in the zooplankton community of the southern coastal waters of Korea were investigated seasonally in May, August, November 2005, and February 2006. A total of 74 taxa were sampled, with an average abundance ranging from 2,426~23,793 indiv./m3, among which Noctiluca scintillans predominated. Noctiluca scintillans, Acartia omorii, Acartia erythraea, Paracalanus parvus s. l., Centropages abdominalis, Tortanus forcipatus, and Pseudevadne tergestina were the most abundant species detected. Zooplankton diversity was high around the inner regions during the summer, but it was relatively low in the stations located in the outer regions in the autumn. Non-metric multidimensional scaling (nMDS) revealed significant differences in the structures of the zooplankton community among the three regions. Our results showed that the seasonal variations in zooplankton communities in the southern coastal waters of Korea were attributable to seasonal changes in temperature, salinity, chlorophyll a concentrations, and N. scintillans blooms; additionally, this particularly study area might have been specifically influenced by the appearance of the Tsushima Warm Current.