Abstract: Based on hypervariable region of mitochondrial control region (D-loop) sequences, we examined the population genetic structure of the bullet tuna (Auxis rochei) collected from seven locations between 5°N to 21°N in the South China Sea. A total of 185 haplotypes were defined from 201 individuals of fishes. The genetic diversity analysis shows that the samples of A.rochei from the seven locations in the South China Sea possessed quite high haplotype diversity (0.958 2~1.000 0) and high nucleotide diversity (0.034 327~0.041 235). The neighbor-joining tree for D-loop haplotypes reveals no significant genealogical clades of the fish samples corresponding to the sampling locations. Analyses of molecular variance and pairwise F_ST suggest most of the genetic variation (98.33%) was attributed to variability within populations. A high rate of gene flow between different populations implies a panmixia for A.rochei in the South China Sea. Both mismatch distribution analysis and neutrality tests indicate a late Pleistocene expansion in A.rochei. The results demonstrate that A.rochei in the South China Sea belong to the same population with high genetic diversity. Thus, a single-stock management regime can be supported in fishery management.