There are four endemic schizothoracins of genus Schizothorax from Nujiang River, in southwestern China, S. nukiangensis, S. lissolabiatu, S. yunnanensis paoshanensis, and S. gongshanensis. Many factors, such as overfishing, habitat degradation and environmental change, have serious effect on their living and propagate, especially the impact from the programming thirteen dams construction at middle and lower reaches of Nujiang River. The study on the population structure and conservation status of those schizothoracins previously was lack. From April 2007 to August 2008, 116 individuals of S. lissolabiatus, 76 individuals of S. yunnanensis paoshanensis, 35 individuals of S. gongshanensis were collected from Nujiang River (The upper Salween River). The complete mitochondrial cytochome b gene sequences were used to evaluate their genetic diversity. The result showed that (i) nine haplotypes and 14 polymorphic sites were found among 116 individuals of S. lissolabiatus. The total haplotype diversity values, Nucleotide diversities were 0.8399±00124, 0.0025±0.0015 respectively,(ii) Three haplotypes and 23 polymorphic sites were found among 76 individuals of S. yunnanensis paoshanensis. Haplotype diversity values, Nucleotide diversities were 0.5544±0.0449, 00080±0.0041 respectively. (iii) eight haplotypes and 13 polymorphic sites were found among 35 individuals of S. gongshanensis. Haplotype diversity values, Nucleotide diversities were 0.7664±0.0556, 0.0017±0.0011 respectively. Due to current environmental pollution, water conservancy, and/or severe fishery, the populations for the three schizothoracins declined and were isolated to small populations. In demographic history of S. lissolabiatus and S. gongshanensis, population had been expanded, and then population declined.The populations of Lanzha River and Dong River (Longwangtan and Beimiao Reservoir) might have been isolated 1.1Ma, and they belong to two evolutionary significant units or separated management units.