Abstract: We examined the population genetic structure and genetic diversity of the frigate tuna (Auxis thazard) in the South China Sea based on mitochondrial control region (Dloop) sequences, using a total of 200 individuals collected from eight sites (6°N~20°N) during March 2013 and April 2015. Fragments of 911 bp were sequenced and a total of 184 polymorphic sites were detected, which defined 191 haplotypes. Genetic diversity analysis shows that A.thazard in the South China Sea were characterized by rather high haplotype diversity (0.999 5±0.000 6) and high nucleotide diversity (0.019±0.009). Phylogenetic analysis reveals no significant genealogical clades of samples corresponding to sampling localities. Analyses of molecular variance and pairwise F_ST suggest a high rate of gene flow and the lack of genetic differentiation among different populations. Both neutrality tests and mismatch distribution analyses indicate a recent population expansion in A.thazard. It is demonstrated that A.thazard in the South China Sea belong to the same population, with strong adaptive capacity and evolutionary potential due to its high genetic diversity. Thus a single-stock management regime could be supported in fishery exploitation and management.