Captive bred fish released to the wild for conservation purposes have low survival. They exhibit a rapid reduction of genetic variability and wild fitness-related behaviours after a few generations in captivity, i.e. hatchery fish are outcompeted for natural food compared to wild conspecifics. These behaviours are controlled by the brain and brain development is influenced by an individual’s genome and the environment. However, it is not yet known how genetic heritage and rearing environment interact to affect brain development in salmonid fishes. To investigate this, we reared hatchery and wild broodstock salmon of the same population under standard and enriched hatchery conditions until 2+yrs. We then measured brain and sub-structure volumes (relative to body size), and individual genetic diversity. We observed larger relative total brain size in salmon of wild broodstock origin and reared under enriched conditions, some key structures such as cerebellum being significantly larger. This indicates that the new enriched rearing method can counteract the negative effects of domestication on brain development. Our results also show differences in brain plasticity as salmon of different genetic backgrounds respond differently to the different rearing environments, possibly as result of differing selection pressures under the different rearing environments. We propose that this may provide clues as to the behavioural deficits seen in hatchery fish released to the wild and provides evidence that enriched rearing can improve wild performance of salmon for conservation releases.