Abstract:To investigate the availability of using COⅠ sequences as DNA barcodes to identify Lethrinus species, partial sequences of mitochondrial cytochrome oxidase subunit Ⅰ (CO Ⅰ) gene of 10 Lethrinus speices from South China Sea were obtained by PCR amplification and sequencing. Combining with COⅠ gene sequence of 2 Lethrinus species from GenBank, a total of 37 individuals COⅠ sequences of 12 Lethrinus species were obtained. The phylogenetic of the sequence was calculated using MEGA5.0, and the molecular phylogenetic relationships were constructed and analyzed using maximum likelihood method.The results showed that intra-specific genetic distance within the 12 Lethrinus species were between 0.000 to 0.005 with the average genetic distance was 0.002, lower than the minimum inter-specific genetic distance of 0.020(2%) for species identification. The inter-species genetic distances among species were 0.074-0.210, with the average genetic distance was 0.155, which was 77.5 times of intra-specific genetic distance, Indicating that the COⅠ gene could be used as the barcode gene for the Lethrinus identification. In the molecular phylogenetic tree, 12 Lethrinus species mainly formed 4 groups. Specie Lethrinus miniatus was first seperated and located at the base of the tree (branch Ⅳ). Following was Lethrinus miniatus which also fromed a single branch (branch Ⅲ). The rest of Lethrinus species were divided into two branches: Branch Ⅰ contained 5 Lethrinus species, most of which were low-bodied and conical teeth; Branch Ⅱ contained 5 Lethrinus species with higher bodies and molariform and submolariform teeth. Results were consistent with the previous studies that Lethrinus species were mainly divided into two groups: one was high bodied with mortar teeth feature and another was low-bodied with conical teeth. It also supported the previous conclusion that the two different types of Lethrinus(low-ied with conical teeth and low-bodied with conical teeth)both evolved from a high-bodied, conical-toothed ancestor like species Lethrinus miniatus.