Accurate identification of fish stocks is essential for the successful management of fishery resources. In this study, the populations of dotted gizzard shad, Konosirus punctatus, which is listed on the International Union for Conservation of Nature red list of the threatened species, were identified by combining two phenotypic methods: otolith shape analysis and comparison of growth parameters. Otolith shape analysis revealed two types of otoliths, pointing to the presence of two gizzard shad stocks in two areas along the Korean coast: the East Sea and the Yellow Sea + western Korean Strait. It is also supported by the result that the two stocks are significantly different in the shape indices (SI), and asymptotic fork length (FL∞). These results may be due to the influence of several environmental factors, such as temperature, salinity, and food availability. Overall, our findings suggest that there are two phenotypic stocks of K. punctatus in the Korean coastal waters and they should be managed differently.