Abstract: We analyzed 711 bp segment of the mtDNA cytochrome oxidase subunit I of 62 individuals of Scomberomorus commerson collected from Raoping, Yangjiang in Guangdong Province and Dongxing in Guangxi Province, among which 26 mutations and 18 haplotypes were detected.Generally, the haplotype diversity (Hd=0.808 0.040) level was relatively high, while the nucleotide diversity was much poorer (=0.004 00.000 6).Three shallow clades appeared in the Kimura 2-parameter based on neighbor-joining tree and parsimony network; pairwise fixation index Fst value ranged from 0.811 to 0.833 ( P0.001) ; gene flow ranged from 0.1 to 0.117. Analysis of molecular variance shows that the genetic variation among three clades was 82.61% , suggesting significantly high genetic differentiation. The deduced divergence time was about 890～226.7 ka BP ( i.e. , during the middle Pleistocene period) , and the Glacial interglacial cycles in Pleistocene might be the reason of genetic differentiation. However, individuals from various locations were intertwined together in all clades; pairwise Fst( -0.027～0.066) and gene flowamong sampling sites revealed no significant differentiation. AMOVA analysis shows that the percentage of population variation was 96.34%, suggesting a relatively high level of gene flow among sampling sites in the South China Sea. In Clade A, the significant negative values of neutral test and the unimodal mismatc h distribution suggest a recent population expansion occurred in this clade about 890 000～226 700 years ago, due to the effects of changed living space and marine currents during Pleistocene glaciations.