Abstract: The genetic diversity of Cheilinus undulatus was studied based on the sequence analysis of mtDNA (COⅠ and Cytb) of 101 individuals from four geographical populations including Lingshui (n=31), Malaysia (n=20), Xisha (n=14), and Nansha (n=36). Using PCR amplification and sequencing, 1560 bp of COⅠand 1141 bp of Cytb sequences were obtained. For COⅠsequences, the number of haplotype is 20, haplotype diversity was 0.629, the nucleotide diversity was 0.00077, the average nucleotide difference was 1.195, and the number of polymorphic site was 23. For Cytb sequences, the number of haplotype was 27, the haplotype diversity was 0.755, the nucleotide diversity was 0.00126, the average nucleotide difference was 1.424, and the number of polymorphic site was 30. AMOVA showed a higher percentage of 73.74% with-population variation than that of 26.26% among-population variation in COⅠsequences. Similarly, the percentage of 95.78% within-population variations was higher than that of 4.22% the among-population variation in Cytb sequences. The haplotype network of COⅠand Cytb genes with stellate radiation structure suggested that haplotypes distribution did not have the characteristics of clear geographical differentiation. Genetic diversity was low and the genetic divergence was inconspicuous between populations of C. undulatus. These results may be very useful to protect this species.