Abstract: Schizothorax wangchiachii, with high ecological and great economic value, is a rare indigenous fish of Jinsha River. The SNP markers of Schizothorax wangchiachii were developed by SLAF-seq technology in this paper. Further analysis on genetic diversity of Schizothorax wangchiachii was also done in this paper. The results showed that 709785 SLAF labels were obtained through SLAF-seq technology, and 243304 were polymorphisms. 777082 group SNP markers were obtained through bioinformatics analysis. 598354 effective SNP markers were collected to analyze the genetic diversity of Schizothorax wangchiachii. The results showed that the observed allele number of wild population was 2.005, and the expected allele number was 1.5272. The observed heterozygosity was 0.2007, while the expected heterozygosity was 0.316. The average genetic distance was 0.1523, while the genetic diversity index was 0.3386. The Shnnon Wiener index was 0.4827, and the PIC was 0.2562. The MAF was 0.2313. The figures showed that the genetic diversity of wild Schizothorax wangchiachii between Ahai section and Longkaikou section was in the medium level. It related to artificial disturbance. Recently, the wild Schizothorax wangchiachii numbers are decreasing. Hence, this research plays an important role in protecting the germplasm resource of Schizothorax wangchiachii.