Polymerase chain reaction (PCR) technique was used to amplify the elongation factor 1-alpha intron sequences region from 95 wild individuals of Penaeus monodon caught from sea waters of Sanya of Hainan, Shenzhen, Zhanjiang and Beihai in the south China Sea. The PCR products were cloned. The electropositive cloned products were sequenced. As a result, about 216 bp nucleotide sequences that could be analysed were obtained (the primer and some of the marginal sequences were exclude). The nucleotide sequences of the black tiger prawn from China combined with sequences of the western Indian Ocean and western Pacific populations (from Genebank) were analysed. By using Clustal X to align and compare the sequences of the 207 individuals with each other , 188 variation sites were observed ,of which there were 67 insertion sites or deletions , 121 polymorphic sites. 89 haplotypes were detected from the elongation factor 1-alpha intron sequences, the Haploid diversity (H_d) was 0.975. The results showed that gene diversity of the China population was minimum, gene diversity of the western Indian ocean was biggest. By analyzing popultion pairwise F_ST-valules, it indicated very strong differentiation between populations from the western Pacific Ocean and western Indian Ocean (P＜0.001), this differentiation was also detected between Chian Sea, western Indian Ocean and western Pacific populations. In the molecular phylogenetic tree constructed in the method of UPGMA, the western Pacific Ocean and Chian populations aggregated into a branch, the western Indian Ocean population aggregated another branch. Judged by sequence difference analysis, the distance related between Chian and western Indian population was farther than the distance related between Chian and western Pacific population; among four population of Chian Sea, Beihai population was more distantly related with Shenzhen, Hainan and Zhanjiang populations, while Shenzhen, Zhanjiang and Hainan populations were more closely related.