Culture of mud crab (genus Scylla) as precious seafood is growing rapidly in China recently. However, the taxonomy of mud crab in China is still in controversial. Mitochondrial cytochome oxidasesubunit I (COI) gene was used to identify species of genus Scylla resided along coast of southeastern China. A fragment of the COI gene was amplified and sequenced from 72 Scylla spp. individuals obtained from 5 regions along coast of southeastern China. 12 distinct haplotypes, which were identified among 72 COI sequences, were above 98% identical to the known S. paramamosain COI gene sequences, and showed 7.36%-15.54% difference from other 3 species. The average genetic distance of COI sequences between these individuals and S. paramamosain is only 0.00783 and this does not significantly differ from the intraspecific distance, while between these individuals and S. serrata, S. olivacea and S. tranquebarica is 0.11659, 0.17812 and 0.08423 respectively. The NJ tree shows that all four species formed reciprocal monophyletic groups, with the S. olivacea located in the base, and S. olivacea closely related to S. tranquebarica. Four species of Scylla are delineated as four well supported groups, with average levels of interspecific sequence difference (-12%) more than six times greater than that observed at the intraspecific level (-2%) and 12 haplotypes identified in this study cluster closely with the known COI sequences from S. paramamosain. The results of sequence characterization, genetic distance and phylogenetic analysis suggest that all samples investigated should belong to S. paramamosain and S. paramamosain should be one of the most common species in China. Caution is called for species identification when studying Scylla.