We studied the genetic diversity of five populations of Paramesotriton caudopunclatus using D-loop sequence of mtDNA as a molecular marker. As a result, we obtained 690 bp long D-loop sequences of 42 samples from five populations collected from Leigongshan and Wulingshan. In the sequences, there were 30 variable sites. Based on these sites 13 haplotypes are defined. No shared haplotype was found among the five populations. P.caudopunclatus populations had high haplotype diversity and low nucleotide diversity. The results of fixtion index (F_ST), nucleotide diversity (D_xy) and migration rates (N_m) analyses indicated that a certain extent differentiation occurred between Leigongshan population and Wulingshan population. In phylogenetic trees, all haplotypes were clustered according to their geographic distribution. Three populations from Leigongshan constituted one clade, while the other two populations from Wulingshan constituted another clade, supporting the treatment of Leigongshan and Wulingshan populations as two separate management units.