Zooplankton community structure was investigated in the Saemangeum region in March, May, July and October of 2007 and 2008 in order to understand the potential effect of post construction of Saemangeum dyke on their temporal and spatial distribution. Mean abundance of zooplankton in the inner and outer area of the dyke, except for dinoflagellate Noctiluca scintillans, ranged from 173 to 15,830 ind.m$^{-3}$, showing higher variability in the inner area compared to the outer area. Zooplankton abundance was higher in the outer area than the inner area in 2007, and vice versa in 2008. In the inner area of the dyke, zooplankton abundance was the highest in May 2007 and March 2008. In the outer area of the dyke, abundance was the highest in October 2007 and July 2008. Brackish species such as Tortanus derjugini and Pseudodiaptomus inopinus were dominant prior to construction of the dyke, and appeared less frequently in the inner area. Marine zooplankton taxa such as juvenile hydromedusa, and calanoid copepods Acartiahongi and Paracalanus parvus s.l. dominated both areas of the dyke. In CCA analysis, zooplankton community structure in the inner and outer area was similar in March and May, but different in July and October. Temperature, salinity and COD were important environmental factors affecting zooplankton community structure. These results suggest that zooplankton community structure in the inner and outer area of Saemangeum dyke are significantly affected by whether the sluice gates are closed or open.