Understanding the population structure of fish species could provide the basic information for utilization andmanagement of fishery. The Red bigeye Priacanthus macracanthus was one of the economically important fish speciesthat was widely distributed in the South China Sea. However, little was known about the populations. In the presentstudy, the population genetic structure and diversity of P. macracanthus were examined in the South China Sea based ona 684 bp segment of the mitochondrial cytochrome b gene. A total of 264 individual samples were collected from sevenlocalities in the northern South China Sea and the Southwestern Nansha Islands. The bases A, T, C, and G had frequenciesof 22.7%, 28.4%, 33.4%, and 28.4%, and A + T content was similar to that of C + G (51.1% and 48.9%, respectively).Ninety-two polymorphic loci were detected and 90 haplotypes were defined. Genetic diversity was high forhaploid type (0.8130–0.9012) but nucleotide diversity was low (0.0040–0.0053). A haploid type network diagram foundadvantages for the Hap1, Hap2, Hap4, and Hap6 haploid types, but no significant geographical features were detected.A pairwise Fst analysis showed that most of the Fst value were low and non-significant (P>0.05). The overall Fst for thetotal sample was only 0.012, which showed little differentiation among populaitons. Analysis of molecular variance(AMOVA) indicated that most of the differentiation occurred within populations (98.75%) and only 1.25% occurredamong populations. Phylogenetic tree constructed using neighbor-joining method showed that the seven groups of P.macracanthus were a panmictic population, with no obvious type branches. Haplotype network using median-joiningnetwork approach also revealed no significant genealogical clades corresponding to sampling localities. Both neutralitytests and mismatch distribution analyses indicated a recent population expansion in P. macracanthus during the last glacialmaximum. These results indicate high gene flow among populations of P. macracanthus and they may belong to asingle population in the South China Sea.