We investigated seasonal changes in the mesozooplankton community structure in November 2006 and February, May, and August 2007 at 12 stations in the semi-enclosed Muan Bay, Korea. Forty taxa were sampled, with an average abundance ranging from 1,459 to 20,078 indiv. $m^{-3}$; the highest abundance was detected in August 2007, and the lowest in February 2007. Acartia omorii, A. hudsonica, A. ohtsukai, Bestiolina coreana, Calanopia sp., Paracalanus parvus s. l., Cirripedia larvae, Decapoda larvae, and Gastropoda larvae were the most abundant taxa detected. The species diversity of the mesozooplankton was high around the inner regions in August 2007 but it was relatively low in November 2006. Non-metric multidimensional scaling (nMDS) revealed significant differences in the structure of mesozooplankton community among the seasons. Canonical correspondence analysis (CCA), performed to examine the relationships among dominant taxa, stations, and environmental variables, showed that most species of copepods were positively correlated with temperature, salinity, chlorophyll a, and COD concentration. Our results suggested that the mesozooplankton community structure observed in this study might be affected partly by the seasonal changes in environmental variables, such as the status of the sluice gates (i.e., open or closed) and the in situ production of resting eggs by major copepods.