Carcharhinus leucas has a cosmopolitan distribution and marked genetic structure. However, analysis of this structure has not included the South China Sea population. In the present study, we collected a total of 23 individuals from Xisha, and Nansha Islands in the South China Sea and a 503 bp segment of mitochondrial DNA control region was sequenced. 17 polymorphic sites were obtained defining 7 haplotypes in the South China Sea population. Contrary to heterogeneous expectation, AMOVA and pairwise FST values showed that the genetic differences in this region were all non-significant. The pattern of population demography showed a stable model in this species in the South China Sea population. To reveal its population structure within the large-scale geography distribution, we added 169 sequences of the mitochondrial control region already genotyped from northern Australia. The South China Sea and northern Australia groups were successfully distinguished by the NJ tree with significant genealogical branches of haplotypes. These results indicated that there might have only one fishery management units of C. leucas in the South China Sea and genetic heterogeneity among C. leucas in the center of Indo-Pacific regions.