The short-term variations of the mesozooplankton community structure were investigated in Gamak Bay during summer season, 2006. The study was based on a comprehensive survey constituting from 12 stations on June 19, July 28, August 4, and August 29, respectively. Mean of temperature and chlorophyll a concentrations in the surface layer were significantly higher than those in bottom layer, and those concentrations were significantly higher in the inner bay than those in the outer bay. A total of 40 taxa including 19 copepods were observed in Gamak Bay during summer season. Mean abundance of total mesozooplankton varied from 1,859 to 26,111 indiv. m-3. The dominant species were Noctiluca scintillans, Penilia avirostris, Evadne tergestina, Paracalanus parvus s. l., Acartia omorii and Cirriped nauplii and cyprii in Gamak Bay, and they contributed 90% of mean abundance of total mesozooplankton. Noctiluca scintillans was high after the rainfall. Cluster analysis showed that the mesozooplankton community could be divided into 4 distinct groups, indicating rapid change of the community in the short-term of this survey. The relative contribution of each group of the N. scintillans, P. avirostris, E. tergestina, and P. parvus s. l. showed differences during the phytoplankton bloom period. The mesozooplankton community compositions were highly associated with water temperature, and salinity in physical conditions, and food organisms affect short-term variations in mesozooplankton composition. Interestingly, protozoa N. scintillans, and Cladocera appeared to be one of the key organisms to extinguish the phytoplankton bloom. Therefore, this study suggests that N. scintillans, and Cladocera could be a key player to control the mesozooplankton community structure during summer season, 2006.