Abstract: We investigated the genetic structure of red bigeye (Priacanthus macracanthus) population in six sampling sites off the South China Sea including five coastal waters of Beibu Gulf, Sanya, Maoming, Zhuhai, Shantou and the Southwest Nansha. Sequences of the mitochondrial control region (D-loop) were amplified by polymerase chain reaction. Fragments of 729 bp of the mitochondrial D-loop were sequenced from 224 individuals, and 101 mutated sites, 94 nucleotide polymorphism sites as well as 172 haplotypes were identified. All the six groups were characterized with high haplotype diversity (0.980 5~ 0.997 1) and low nucleotide diversity (0.048 2~0.060 9). Analyses of phylogeny, molecular variances and pairwise Fst showed no significant genealogical clades or clusters of samples corresponding to sampling localities. Both neutrality tests and mismatch distribution analyses revealed a recent population expansion in P.macracanthus. Thus, the six P.macracanthus groupsin the South China Sea belong to one population. The results provide references for the fishery resources sharing and quotas winning between China and the South China Sea surrounding countries.