Abstract: Polymerase chain reaction (PCR) technique was used to amplify the mtDNA 16S rRNA gene and control region from 20 wild individuals of Penaeus monodon caught from Sanya of Hainan. The PCR products were purified and sequenced As a result, a 495 bp sequence of mtDNA 16S rRNA gene and a 470 bp sequence of mtDNA control region were obtained (some of the marginal sequences were excluded). The sequences were then aligned and analysed by Clustal X and ARLEQUIN 2000. 17 polymorphic sites and 8 haplotypes were detected from the partial mitochondrial 16S rRNA sequences while 100 polymorphic sites and 17 haplotypes were detected from the partial mitochondrial control region sequences. The haplotype diversity (H) and the nucleotide diversity () were 0.7000 and 0.0045 respectively among 20 individuals of P. monodon based on the partial mitochondrial 16S rRNA sequences, while H and were 0.984 and 0.0480 respectively based on the partial mitochondrial control region sequences. In conclusion, application of mtDNA 16S rRNA analysis in P. monodon population genetic diversity study may be limited. However, mtDNA control region is an ideal marker for analysis of P. monodon population genetic diversity.