Abstract
Brachymystax lenok tsinlingensis is an endangered freshwater fish which is endemic to part of China. To investigate its genetic diversity and population structure, mitochondrial cytochrome b gene and D-loop control region were used to analyze samples from five different locations. Fifteen haplotypes were identified; however, no shared haplotypes were observed among different streams. The analysis of molecular variance (AMOVA) results indicated that 77.38% of total variation was attributed to differentiation between populations, whereas 22.62% from variation within populations. The high genetic differentiation among the populations would provide useful information for building natural reserves and artificially releasing cultured juveniles in the future.