In order to confirm the genetic relationship between the Yellow Sea and East China Sea populations of mantis shrimps Oratosquilla oratoria, fragments of mitochondrial DNA COI gene samples were analysed. A total of 212 individuals from nine localities in the East China Sea and Yellow Sea were collected and 108 haplotypes were detected. Neighbour-joining analysis revealed a complete genetic break between the Yellow Sea and East China Sea, which was consistent with the previous mtDNA 16S rRNA. Pleistocene isolation and the current physical barrier were responsible for the complete genetic break between the East China Sea and Yellow Sea. Furthermore, local adaptation in the COI gene may also be contributed to by the genetic differentiation between the populations of the Yellow Sea and East China. The different Ka/Ks ratios between the two clades may reflect different selection pressures and local adaptation on the fragment of COI gene.