We investigated the distribution and species composition of zooplankton in relation to hydrographical characteristics in the Korea Strait during the winter (February) and summer (July) of 2009. Satellite images of sea surface temperatures and in situ CTD data showed that the southeastern water zone (St3-5) off Jeju Island was strongly influenced by the Tsushima Current during both the winter and summer, whereas the Changjiang Diluted Water, characterized as water with relatively low salinity, was evident in the coastal waters of Jeju Island during the summer. During winter, zooplankton abundance was significantly higher than in the summer, with dominance by copepods, ostracods, siphonophorans, appendicularians, and nauplii. In both seasons, copepods represented >70% of the total zooplankton population. Calanus sinicus, a large calanoid copepod, was dominant in near the coast, and that may be associated with the intrusion of low salinity water (i.e., the Changjiang Diluted Water) along the coast. The abundance of P. parvus s.l. and A. omorii, known as neritic copepods, was mainly associated with the Korea Southern Coastal Water. Foraminiferans, Ostracods, O. plumifera, and P. aculeatus were concentrated in the southeastern water off Jeju Island during both seasons; showing their association with the Tsushima Current, which is characterized warm, high salinity water. Our results suggest that the distribution, abundance, and species composition of zooplankton are highly influenced by different water masses in the Korea Strait.