Abstract: To study the genetics and evolution of the genus Brachymystax at the national geographic scale from the perspective of InDel in genome-wide, we employed whole genome resequencing and InDel detection analysis on six Brachymystax populations (a total of 90 samples) collected from Shaanxi, Gansu, Xinjiang, Hebei and Heilongjiang. The aim was to provide new insights into the genetic differentiation and local adaptation of Brachymystax populations through the perspective of InDels. Results showed the detection of a total of 3056034 high-quality InDel mutation sites among the six Brachymystax populations, with deletions exceeding insertions. After standardizing various gene regions, it was observed that intronic regions exhibited a relatively higher concentration of InDel sites. A total of 1715464 fixed InDels were identified in all branches of the phylogenetic tree, accounting for 56.08% of the total, primarily situated at the base of each lineage. Population structure analysis revealed that each geographic population of Brachymystax displayed a relatively distinct genetic structure. Regarding adaptive analysis, 621 candidate selection genes associated with local adaptation were detected using population branch statistics. Notably, two deletions affecting exonic sequences were identified, resulting in the loss of two and one amino acid codons in insr and dnhd1, respectively. Enrichment analysis of all potentially selective genes highlighted their significant involvement in pathways such as neural development and metabolism. This study provides foundational information for the comprehensive exploration of candidate adaptive genes in the mountain stream habitats of Qinling lenok, alongside facilitating the development of molecular markers for artificial breeding and conservation efforts. Additionally, it serves as a reference for further clarification of species differentiation within the genus Brachymystax.