Abstract: The PCR technique was used to analyze the mtDNA control region sequences in 20 individuals of P.monodon in Shenzhen's sea area. A series of nucleotide fragments with about 650 bp were obtained. The PCR products were purified and sequenced. As a result, a series of 526 bp nucleotide sequences of partial control regions were obtained. The 20 sequences were arranged in counterpoint by Clustal_X software. And then, comparing the control region fragments with each other by Mega software, 114 sites were variable among all the partial mitochondrial control region sequences including 84 parsimonious message sites and five deletion / insertion sites. The relative genetic distances were calculated among individuals by Pairwise distance method of Mega. The results indicated that the differentiation of the 20 sequences ranged from 0.010 to 0.054 and showed 20 kinds of haplotypes among 20 individuals. The UPGMA and NJ phylogenetic trees were established by the cluster analysis. The number of polymorphic sites (S) was 114; the nucleotide diversity (Pi) and the average number of nucleotide differences (K) were 0.05278 and 27.500, respectively. It can be concluded that the variation in mtDNA control region sequences of P.monodon in Shenzhen's sea area was greater relatively. So the genetic diversity of P.monodon in Shenzhen's sea area was higher relatively. As a result, mtDNA control region sequences can be used to scan genetic diversity of populations.