Abstract: The naked carp（Gymnocypris przewalskii） has gradually adapted to the special plateau geography of Qinghai Lake during the long-term evolutionary process. In order to reveal the adaptive evolutionary mechanism of G. przewalskii, GBS（genotyping by sequencing） was used to screen 72 naked carp from 6 populations for outlier SNP（single nucleotide polymorphism） markers to explore the possible effects of natural selection on them, to explore the related SNP sites that may be affected by Natural selection, and to conduct Sequence alignment and functional annotation on the contigs where the discrete SNP contigs sites are located. A total of 1 566 highly variable adaptive outlier SNP sites were identified in the study. NR（non-redundant protein sequences） annotation showed that the top two species with the highest proportion of similar sequences were Anabarilius graham and Cyprinus carpio, respectively. GO annotation analysis revealed that more contigs were annotated to cellular process, metabolic process and binding. KEGG annotation analysis showed that the most contigs were annotated to metabolic pathways and neuroactive ligand-receptor interaction pathways. Among them, genes annotated to metabolic pathways included ctu1, cps1, gba2, fasn, plcg1, etc., which may be associated with the local adaptation of Gymnocypris przewalskii. The results demonstrate that G. przewalskii may have developed local adaptations related to environmental factors such as temperature and salinity, and provide technical methods and data to further explore the local adaptation mechanisms of G. przewalskii.