Interbreeding between domesticated and wild animals occurs in several species. This gene flow has long been anticipated to induce genetic changes the life history of individuals with mixed genetic ancestry, and thereby influencing population dynamics and viability. We show that individuals with high levels of introgression (domesticated ancestry) have their complete life-cycle altered in natural populations of Atlantic salmon Salmo salar. Introgression increased the probability of early smoltification and seaward migration, and altered the age-specific probability of maturing and migrating back to the river, as well as increased the growth both in freshwater and at sea leading to an increased age-specific size at maturation. Our study document widespread changes in the complete life-cycle of the wild Atlantic salmon following gene flow from a selectively bred, domesticated conspecific. The continued high abundance of farmed escapees threatens the wild Atlantic salmon by inducing genetic changes in important traits related to fitness.