This study examines the genetic diversity and adaptive evolution of Ctenopharyngodon idella populations across Asia, aiming to enhance our comprehension of the molecular evolution mechanisms and immune adaptations in C. idella. We conducted whole-genome resequencing of C. idella populations from four Chinese provinces (Hunan, Chongqing, Tianjin, Guangdong) and three Asian countries (Nepal, Vietnam, India). Employing population genetics methodologies, we analysed population structure, performed principal component analysis, constructed phylogenetic trees, assessed genetic differentiation, and conducted selective sweep analyses. The Wanzhou population displayed the highest genetic diversity, whereas the Nepal population exhibited the lowest. Cluster analysis revealed significant genetic similarities among the five populations in Vietnam and China. A total of 6 548 523 SNP sites were identified, predominantly in intergenic regions and enriched in signaling pathways such as cell adhesion molecules, hematopoietic stem cells, and DNA recombination repair. Selective sweep analysis highlighted genes enriched in pathways related to immune response regulation, cardiomyocyte regulation, and sodium ion channel activity. Utilizing SNP annotation data, we identified gimap8 in Indian and Nepal populations, crucial for T cells and B cells development. C. idella populations in Anxiang, Yuanjiang, and Wanzhou in China, are genetically diverse, while those in Nepal and India show significant differentitation from other populations. We preliminarily identified the potential adaptive genes gimap8. Concurrently, mutations in gimap8's base affected the gene's structure in three populations. This study lays a foundation for further exploration of the molecular evolution mechanism of C. idella in various habitats, reflecting the molecular mechanisms by which C. idella populations adapt to different environmental stresses. The results reveal the differences in the molecular mechanisms of adaptive immunity in different C. idella populations. These findings not only deepen our understanding of C. idella's adaptive evolution in diverse environments but also provide a significant theoretical basis for C. idella breeding and offer new insights.