AbstractThree primary factors affecting genetic patterns of marine species in the Northwestern Pacific Ocean have been proposed: isolation and population expansion during Pleistocene glacial cycles, ocean currents facilitating the gene flow, and the Yangtze River outflow imposing a physical barrier to gene flow. Here, we examined these factors affecting population structuring of the Asian paddle crab, Charybdis japonica, in the Yellow Sea, East China Sea, and adjacent areas. Genetic variation in nine populations of C. japonica (n = 169) was determined from partial mitochondrial cytochrome c oxidase subunit I sequences. Among the 14 haplotypes identified, a dominant haplotype H1 was present in all populations, and a relatively abundant localized haplotype H2 was found in four of the northern populations. Furthermore, the frequency of the common haplotype H1 decreased from south to north. A genetic discontinuity was detected in Haizhou Bay, which divided species into two groups (north group and south group). The lack of genetic structure in the south and north groups indicates high dispersal of C. japonica within groups. Local marine gyres in Haizhou Bay might be responsible for the divergence of the north and south groups. Our study highlights the importance of local marine gyres for influencing genetic structure in marine coastal species in the Northwestern Pacific, especially in species spawning inshore.