To test the hypothesis that specific epigenetic variations are associated with captivity, we compared the genome-wide pattern of methylation in hatchery-reared Coho Salmon (Oncorhynchus kisutch) with that of their wild counterparts in two geographically distant rivers in British Columbia, Canada, using a reduced representation bisulfite sequencing (RRBS) approach. This is the first study to demonstrate that captive rearing induces epigenetic modification in parallel which could provide a potential mechanism for rapid adaptation to hatchery environment