Abstract: 【Objective】To investigate the genetic diversity of the farmed brown trout（Salmo trutta）populations in Xinjiang and Tibet，and to analyze the relationship and genetic differences of brown trout in the two places，so as to lay a foundation of data and methodological basis for molecularly-assisted breeding of brown trout.【Method】The next-generation high-throughput sequencing technology was applied to re-sequence the genomes of 2 brown trout populations（12 individuals from each）collected in Dabancheng，Xinjiang，and Yadong，Tibet. Population structure，genetic diversity and selective sweep were analyzed according to the identified single nucleotide polymorphisms（SNPs）of each individual. 【Result】A total of 4694474928 Illumina reads were generated in the two populations by whole genome resequencing， with which 8559684 SNP loci were identified referencing the brown trout genome. SNP-based analyses revealed that the genetic diversity of Tibetan population was slightly higher than Xinjiang population. Analyses of phylogeny，population structure and principal components exhibited a close relationship between them，while the linkage disequilibrium decay analysis displayed that the Tibetan population were under more selection pressure. Selective sweep analysis based on the calculation of F_ST and Pi values revealed significant selection signals were mainly on chromosomes 5 and 19 of the Xinjiang population and on chromosome 17 and 18 of the Tibetan population. Among 94 genes localized in these regions，21 （17 from the Tibetan population and only 4 from the Xinjiang population）were annotated as immunity- or disease-related genes.【Conclusion】The Xinjiang and Tibetan brown trout originate from the similar lineages with little genetic diversity. The Tibetan population undergoes more environmental selection than the Xinjiang population does.