fish, and used to be an important object for bottom trawl, bottom gillnet fishing in South China Sea. Due to the degradation of habitats and overfishing, the quantity of this fish has been decreased greatly in recent years. The recent studies on mainly focused on the chromosome, fisheries resources survey as well as phylogenetic relationship for terapontid fish based on gene and 16S RNA , there is no genetic investigation reported. In the present study, the control region of mtDNA of 80 individuals of 5 populations collected from Jieshi, Yangjiang, Linggao and Lingshui, were sequenced to analyze genetic variation in South China Sea, of which 42 mutations and 60 haplotypes were detected in the 951bp sequences. Overall haplotype diversity and nucleotide diversity were relatively low (=0.009±0.000), of which the nucleotide diversity () of Lingshui population is the highest (0.010), and Dongxing population is the lowest (0.008). Apart from 8 haplotypes shared by various populations, the remaining ones were endemic to each population. In the Kimura 2–parameter based neighbor-joining tree and parsimony network, haplotypes from various locations were intertwined together, and no deep lineage branches found, suggesting no obvious phylogenetic and geographical structure. Pairwise fixation indexes among 3 populations from mainland China coastal waters ranged from >0.05), and gene flow from 14.54 to 27.84.values between 2 populations from Hainan Island was >0.05), and gene flow was 5.68. However among the mainland coastal populations and Hainan Island populations ranged from 0.0616 to 0.135 3 (<0.05), gene flow were 1.868 63.808 4, indicating that there were no obvious genetic differentiation within the mainland coastal groups and within Hainan Island groups, but there were medium but statistically significant genetic differentiation between the mainland coastal populations and Hainan Island populations( mainly lives in shallow waters, and juveniles often attach to floating weeds, which may be drifted away along currents. The high dispersal potential and the absence of obvious geographic barriers may cause genetic homogeneity within mainland group and within Hainan island group. However Qiongzhou Strait formed after the separation between the mainland and Hainan Island causes the general trend direction of the annual current from east to west in high strength, promoting the differentiated between the mainland group and Hainan island group, as such there are two management of protected units, Lingshui population were recommended to be protected in priority owing to its highest nucleotide diversity. The significant negative values of neutral test (Fu’s =<0.05), the unimodal mismatch distribution and atypical star-shaped distribution of haplotypes in the parsimony network all suggested a recent population expansion, and the deduced expansion time was 120.636.2 ka BP (i.e., during the late Pleistocene), effective population size after the expansion was about 8.7×10⁶ times larger than before, which probably related to fluctuated sea levels and temperature during the late Pleistocene epochs.