Abstract: Brachymystax lenok tsinlingensis is one type of endemic fishes distributed in Qinling Mountains. Due to the environmental deterioration and overfishing, the size of its population has decreased sharply. To rescue this species it is necessary to study its genetic structure and phylogeography and hereby obtain better understanding of the population. In this study, we determined the genetic diversity of cultured and wild Brachymystax lenok tsinlingensis populations by analyzing their mtDNA Cyt b and D-loop genes. The results showed that the average contents of A, T, C and G in D-loop were 31.9%, 31.6%, 20.8% and 15.7%, respectively. The contents of A+T (63.5%) were higher than those of C+G (36.5%). In the Cyt b gene, the average contents of A, T, C and G were 24.6%, 28.2%, 31.6% and 15.6%, respectively. The contents of A+T (52.8%) were also higher than those of G+C (47.2%). We observed that 43 wild individuals had 18 haplotypes, and that 43 cultured individuals had 24 haplotypes. The two populations shared 8 haplotypes in common. The average haplotype diversity and nucleotide diversity of the wild population (h=0.9070.026; =0.002870.00074) were lower than those of the cultured population (h=0.9170.035; =0.003490.00083). The AMOVA analysis showed that the molecular variation between the two populations was 98.37%, and the variation within a population was 1.63%. The level of genetic differentiation was low (Fst=0.01631, P=0.1075; Nm=30.16). Phylogenetic tree based on NJ and minimum spanning network for Brachymystax lenok tsinlingensis showed that individuals within the two populations did not form a monophyletic clade. Our results suggested that there was an efficient gene flow between the cultured and the wild populations, and there was no significant genetic differentiation between the two populations.