Abstract: To evaluate the habitat preference of Brachymystax lenok tsinlingensis, fishes were caught for the habitat analysis from 25 sampling sites of Longxian and Qinzhou National Nature Reserve in June 2013. In total, 130 individuals were captured in 25 sites with the average density (0.10±0.07) ind./m. There was significant difference in the density between two reserves. The fish density was positively correlated with slope, number of fall/pool, elevation, roughness, coverage, zoobenthos biomass, and velocity and it negatively associated with the river width, depth and dissolved oxygen. Redundancy Analysis (RDA) indicated that five key environmental factors (slope, roughness, coverage, elevation and number of fall/pool) influenced the distribution of Brachymystax lenok tsinlingensis. Habitat suitability curve was established based on the five measured factors, and the best ranges of them were 5%-10% slope, 1500-2000 m altitude, 0.3-0.4 roughness, 12-18/100 m fall/pool, and more than 0.5 coverage, respectively.