Ctenophyngodon idella is one of the most important aquaculture species in the world, and suffered from local adaptation during the process of introduction and aquaculture. However, most studies of C. idella local adaptation were based on genetic variation, and the effect of epimutation was still widely unknown. In order to explore how DNA methylation affects the domestication and environmental adaptation of the C. idella populations in Asia. A whole-genome bisulfite sequencing was performed between 5 farmed populations and the wild background population, followed by further differential methylation analysis and enrichment analysis. A total of 308.15 Gb sequencing data were generated with a sequencing depth of 31× and a mapping rate of 62.97 % in average, where 76 422 differentially methylated loci (DML), 3 737 differentially methylated regions (DMR), and 1 950 differentially methylated genes (DMG) were identified. Gene Ontology enrichment analysis showed that the DMGs were significantly enriched in development process, such as angiogenesis, neural crest cell migration, and cranial skeletal system development. Annotation with the KEGG pathway database exhibited these genes were mainly involved in adhesion junction, Notch signaling pathway, and Wnt signaling pathway. Among the DMG, some might be functional in the developmental process of neural, immunity, bone, and muscle tissues, like sema3d, sema5bb and nrg2a. This study enhances the understanding of the epigenetic mechanism of domestication and environmental adaption during the process of aquaculture and provides valuable data for the conservation and utilization of the C. idella germplasm resources.