The gizzard shad Konosirus punctatus is a fish that is a member of the herring family, Clupeidae, which is native to the estuarine regions of Korea, and distribution of this species is in the coastal areas of Eastern Asia, including China, Japan, Taiwan, and Hong Kong. Previous study reported that there are two distinct mitochondrial lineages of K. punctatus around Korean and Japanese coastal waters: Lineage A was only distributed around Korean coastal waters and dominates the West Sea and South-West Sea group of Korea. While Japanese groups of K. punctatus were exclusively assigned to lineage B. To investigate how genetic differences influence the outcome of secondary contact, genetic polymorphism in Gizzard shad, collected from wild populations of six locations in Korea and four locations in Japan, were examined using eight microsatellite loci, which were developed for the present study. Consistent with previous results, we find distinctive population structure of K. punctatus between Korea and Japan. The results of msDNA reveals that genetic exchange have been existed on the sympatric zones of both lineages in southeast and east coasts of Korean coastal waters. Consequently, the results from the present study will be useful for effective management of this species.