Mantis shrimp (Oratosquilla oratoria) is an important fishery species in coastal areas of China. To exploit and manage this species scientifically, it is necessary to investigate genetic diversity and discuss genetic structure of O. oratoria. In this study, the method of sequences analysis of mitochondrial cytochrome oxidase subunit Ⅰ (COⅠ) gene was used to reveal genetic variance of O. oratoria from the East China Sea (including Miaozihu Island, Nanjiushan, Dachen Island and Nanji island Sea areas, and sample size of each location is 25) and comparative analysis with that of the Yellow Sea and Bohai Sea population and the South China Sea population (gene sequences were obtained from GenBank) was also studied. 658 bp of COⅠ partial sequences of O. oratoria from the East China Sea were obtained by using PCR amplification and sequencing. The results showed that the number of variable site, haplotype, haplotype diversities and nucleotide diversities were 60, 60, 0.963 ± 0.011 and 0.005 94 ± 0.000 44 respectively in all sequences of four geographical populations from the East China Sea, which indicated that O. oratoria was characterized by higher haplotype diversity and higher nucleotide diversity (Table 2). A shallow topology of haplotype neighbor-joining (NJ) tree showed no phylogeographic structure among four geographical populations from the East China Sea (Figure 1). Analysis of molecular variance (AMOVA) suggested the genetic variance mainly came from individuals within populations (Fst =﹣0.007 78, P > 0.05) (Table 3) and F-statistics (Fst) among four geographical populations from the East China Sea showed that no significant genetic differentiations were detected (Fst=﹣0.016 53~﹣0.009 08, P > 0.05) (Table 4). It was supposed that gene exchange in some degree occurred among four geographical populations from the East China Sea. In contrast to gene sequences from the Yellow Sea and Bohai Sea population (30 sequences obtained from Genbank) and the South China Sea population (25 sequences obtained from Genbank), however, two significant distinct lineages was detected from haplotype neighbor-joining tree (Figure 2), and analysis of molecular variance suggested the genetic variance mainly came from individuals among populations (Fst =﹣0.849 71, P < 0.01) (Table 5). Significant genetic differentiations were detected (Fst= 0.884 58，P < 0.01) between population from the East China Sea and population from the Yellow Sea and Bohai Sea, and the situation between population from the East China Sea and population from the South China Sea is the opposite (Fst =﹣0.020 44, P > 0.05) (Table 6). The genetic structure pattern of O. oratoria may be caused by marine environmental conditions or historical climate change. In conclusion, the Yellow Sea and Bohai Sea O. oratoria should be considered as one stock while the East China Sea O. oratoria and the South China Sea O. oratoria should be considered as one stock in their assessment and management based on this article.