Abstract: The RAPD method was explored to analyse the genetic diversity in Heihe River and Xushuihe River populations of Qinling Brachymystax lenok to evaluate their genetic structure scientifically.The proportion of polymorphic loci, mean expected heterozygosity and Shannon′s index of the Heihe River population were 25.8%, 0.1782 and 0.6520, respectively, and those for the Xushuihe River population were 23.4%, 0.1526 and 0.05214, respectively. The genetic similarities within the Heihe River and the Xushuihe River populations were 0.9495 and 0.9549, and their genetic distances were 0.0664 and 0.0556. The genetic distance between the two populations was 0.0152. The genetic diversity of the two populations was relatively low.