Tylototriton kweichowensis is endemic to China and is listed as a category Ⅱ species of the state key protected wildlife. Its distribution area is extremely limited. To study the genetic diversity and its genetic variation of T. kweichowensis populations,we sequenced the complete mitochondrial DNA D-loop ( mtDNA control region) and tRNA^Phe of 58 samples obtained from 12 populations. Only 16 variable sites were detected in the nucleotide sequences of 808 bp,and 26 haplotypes were identified. T. kweichowensis populations have high haplotype diversity and low nucleotide diversity. Neither the estimate of Tajima’s D nor that of Fu and Li’s D deviated significantly from the neutral selection hypothesis for 12 populations. Phylogenetic trees and Median joining Network analysis demonstrated that all the haplotypes could not be clustered to corresponding geographic clades,but showed disordered distribution pattern. There are signs of genetic divergence between Shuicheng population and anyone of others,according to gene flow N_m < 1. In general,there is no distinctive geneticdivergence among its populations.