The genetic variation and structure were analyzed in populations of the Yellow Sea (Lianyungang), the East China Sea (Nanjiushan, Nanji island and Fuzhou) and the South China Sea (the Pearl River Estuary) in mantis shrimp Oratosquilla oratoria by the partial mitochondrial DNA cytochrome b gene in order to promote sustainable utilization of this resources and protect its genetic diversity. All geographical populations had haplotype diversity of 0.9760.010 and nucleotide diversity of 0.039 250.019 13, with the maximal haplotype diversity of 0.9870.035 in Fuzhou population and the minimal haplotype diversity of 0.9310.046 in population of Nanji island, and the maximal nucleotide diversity of 0.064 840.033 02 in population of the Pearl River Estuary and the minimal nucleotide diversity of 0.003 590.002 17 in population of Lianyungang. Analysis of molecular variance showed that 73.88% of genetic variance was derived from individuals among groups, with highly significant genetic differentiation(P<0.01), and without significant genetic differentiation within populations of Lianyungang, East China Sea, and the Pearl River Estuary (P>0.05). The fixation indices (F_(st)) indicated that there was significant genetic differentiation between populations of Lianyungang, and population of the Pearl River Estuary and the other populations (P<0.05). The Neighbor-Joining haplotype tree and reduced median network analysis revealed that there were three distinct lineages (A, B, and C), and highly significant genetic differentiation among the lineages (F_(st)=0.695-0.842, P<0.01). Neutrality tests and mismatch distribution analysis indicated that lineage C recently experienced a population expansion, around 110 000 years ago. In summary, the genetic structure pattern of mantis shrimp appears to have been caused by ocean environment and its life history traits, while phylogeographic pattern appear to have been caused by climatic changes since the Pleistocene. The findings suggest that mantis shrimp from the Yellow Sea, the East China Sea and the South China Sea be considered as three stocks in their assessment and management.