Migratory trout (sea trout) and sedentary trout (freshwater trout) coexist and interbreed. However, the mechanisms underlying the development of the migrant morphotype are still unclear. At one point parr–smolt transformation is initiated and, as a result, juvenile trout are ready to leave the river and migrate to the sea. The smoltification process has been linked to various factors such as body size, growth rate and the physiological state of the fish. In addition, the process is also strongly influenced by environmental factors such as year, seasonality, water temperature and flow rate. For example, hatchery environment can depress the natural parr–smolt transformation and consequently, the success of the seawater migration of reared trout from these hatchery programmes might be adversely affected. We have investigated whether changes in DNA methylation, by means of MSAP (methylation-sensitive amplified polymorphism), could be involved in anadromy. We identified dramatic differences in genome-wide methylation patterns between hatchery reared and seawater brown trout. Furthermore, we demonstrated that salt enriched diets can trigger short-term genome-wide methylation changes in hatchery reared trout. However, these changes only lasted for a short period of time. Determining the duration of this effect could result in increased survival of hatchery-reared trout in seawater when fed on salt-enriched diets. Altogether, these results suggest that salt-induced alterations in DNA methylation patterns could play an important role in enabling fish acclimation to seawater conditions, potentially with important economic consequences for fish farming.