Abstract: To investigate the genetic diversity and genetic differentiation of natural resources of Gymnocypris przewalskii, and provide references for its conservation measures, we collected 72 individuals of G. przewalskii from six natural populations in Qinghai Lake to analyze the genomic SNP and genetic characteristics by using simplified genome sequencing. Altogether 1 600 061SNP markers were obtained, and 45 266 high-quality SNP loci were screened for genetic analysis after filtering. The average P_i diversity index was 0.317 0–0.327 4. The average observed heterozygosity (H_o) and expected heterozygosity (H_e) were 0.459 4–0.482 3 and 0.336 7–0.344 4, respectively. The genetic distance (D) was 0.018 4–0.023 3 and the genetic differentiation index (Fst) were not significant (P>0.05). AMOVA analysis shows that the genetic variation was 102.37% within populations. Further-more, both population structure and phylogenetic tree analysis show that the six G. przewalskii populations clustered into one glade with similar genetic structure. In contrast, the genetic structure obtained from DAPC analysis was relatively clearer, showing that the Haergai, Heima and Shaliu River populations cross-clustered with each other, while the remaining three populations clustered into three other branches. In conclusion, the observed heterozygosity of the six geographic populations was higher than the expected value, with a homogeneous population structure.