In this study，the genetic diversity and genetic differentiation of a total of 82 individuals from three Triplophysa xiangxiensis populations which were sampled from three caves in Wulongshan mountain were evaluated using mitochondrial DNA (mtDNA)， cytochrome b(Cytb) gene and control region (D-loop) sequences．1 140 bp of the mitochondrial Cytb partial sequences and 934 bp of D-loop partial sequences were obtained．No genetic variation was found in cyt b， and all sequences were identical， the contents of T,C,A,and G nucleotides occounted for 28.3%，28.6%，28.1%，15.0%．In the control region，the sequence analysis of the 73 samples revealed 7 haplotypes with haplotype diversity ranging from 0.083 to 0.282．6 polymorphic sites were found from all samples，and all were singleton variables．Seven haplotypes were detected among the sequences，with one of them (haplotype 1) being popular which was represented by 73 individuals．As for annual samples, sequences of all individuals from year 2008 were completely identical except one，and four and five haplotypes were determined from specimens of year 2009 and 2010，respectively．The nucleotide diversisty ranged from 0.000 09 to 0.000 32，respectively．All of which revealed that the genetic diversity in these three T. xiangxiensis populations was low．Analysis of molecular variance(AMOVA) revealed that 100.89% of the genetic variability occurred within annual temporary samples，and negative value of 0.89% came from among temporary samples．The network constructed by sequences of control region displayed a star like topology，with the haplotype 1 in center and the other haplotypes connecting with it by one step of mutation．