The small yellow croaker (Larimichthys polyactis), which is among the most important fishery resources in the northwestern Pacific, is distributed in the Yellow Sea (YS) and East China Sea (ECS). Although many studies have analyzed effective measures for managing L. polyactis, its population structure differs depending on the type of marker. To resolve such discrepancies among markers, we analyzed the population structure of 48 L. polyactis individuals collected from three locations in the YS (off Yeonpyeong-do and Yeonggwang, Korea, and Dandong, China) and one location in the northern ECS (off Jeju Island, Korea) using multiplexed intersimple sequence repeat genotyping. A total of 58,340,434 raw reads were obtained, and 42,587,565 were identified after filtering. Phylogenetic analysis using 88,672 SNPs revealed a great distance between two Dandong individuals and individuals from the remaining locations. Two other Dandong individuals also showed slight separation. The results of structural analysis based on 3,996 SNPs demonstrated an optimal ∆K for K = 5. Three of the five genotypes appeared in all locations, and two genotypes were identified only in four individuals from Dandong. These results suggested that there may be five populations of L. polyactis from YS and ECS: two populations with limited distributions in the northern YS, and three populations tending to mix across northern YS and northern ECS (58.3-75.0%), with some showing hybridization (16.7-58.3%). Therefore, joint management between Korea and China is required for L. polyactis, and a separate policy in each country is required for the protection of local spawning grounds.