<p>The Asian paddle crab, <i>Charybdis japonica</i>, is a commercially and ecologically important marine species. Discerning the population genetic structure and connectivity of <i>C. japonica</i> in a dynamic marine environment is crucial for implementing sustainable management practices. This study investigated the population genetics of <i>C. japonica</i> in the Bohai, Yellow, and East China Seas using 104 mtDNA control-region sequences; a total of 26 haplotypes were identified. High haplotype but low nucleotide diversity were detected among five populations. The frequency of the dominant haplotype H4 declined along the Chinese coast from the southern regions (Taizhou and Zhoushan) to the northern regions (Lianyungang, Yantai, and Dalian). The relatively abundant H1 haplotype exhibited a higher localized frequency in the south than in the north. A Neighbor-Joining phylogenetic tree was constructed from these sequences; two distinct lineages (A and B) with remarkable differences in their geographic distribution frequencies were detected. The proportion of lineage A individuals declined along the Chinese coast from south to north, and lineage B members were mainly found in the Dalian population. AMOVA and pairwise <i>F</i>_ST values showed statistically significant genetic differences among five populations, with the Dalian population differing most from the other four. The Mantel test results indicated that coastal distance may hinder gene flow between Dalian and the other four populations. Thus, our results suggest that five <i>C. japonica</i> populations along the Chinese coast can be considered separate fishery management units. These findings can help guide the design of future <i>C. japonica</i> management practices applicable to this region of China’s coastal waters.</p>