Abstract: Four wild Schizothorax lissolabiatus Tsao populations of 60 individuals were collected from Miaowei-Gongguoqiao Reservoir area, Huangdeng-Dahuaqiao Reservoir area, Lidi section, and Wunonglong section to analyze the genetic diversities using simplified genome sequencing. The results showed that the RsaⅠ-HaeⅢ enzyme digestion efficiency was 87.19%. A total of 240.29 Mreads were obtained. Through bioinformatics analysis, 474390 SLAF tags were obtained with an average sequencing depth of 255.26X. There are 252623 polymorphic SLAF labels. A total of 1151083 SNP markers were obtained. The average SNP integrity was 36.66%, the average heterozygosity of SNP was 9.5%, the average sequencing Q30 was 94.96%, and the average GC content was 39.80%. The observed allele number in the four wild populations was 2, and the average expected allele number was 1.4211—1.5029. The average observed heterozygosity was 0.2381—0.3131 and the average expected heterozygosity was 0.2690—0.3115. The average Nei diversity index was 0.2868—03248 and the average Shnnon Wiener index was 0.4269—0.4811. The average MAF was 0.1854—0.2216 and the average polymorphic information content was 0.2237—0.2553. AMOVA analysis showed that the genetic variation was 89.73% within populations while it was 10.27% among populations. Genetic differentiation indexes (F_st) were –0.0253150—0.1299 (P<0.05), indicating various degrees of differentiation among populations. The genetic distance between the four geographic groups was 0.05—0.15. UPGMA clustering showed that Miaowei-Gongguoqiao Reservoir, Huangdeng-Dahuaqiao Reservoir and Lidi populations were clustered into one glade due to relatively close genetic distances, while Wunonglong population was separated into another class. To sum up, the genetic diversity of the four groups was at the medium level. The genetic distance and clustering results were consistent with the geographical distance of the test population. These results can provide a reference for molecular genetic breeding and germplasm protection of Schizothorax lissolabiatus Tsao.