Atlantic salmon (Salmo salar) have experienced population declines across their native range. Widespread stocking has been a population recovery strategy, but there is a growing awareness that stocking may put genetic integrity at risk. In Prince Edward Island, Canada, over 37 million salmon have been stocked since 1880. This study used a panel of six microsatellites and next-generation sequencing to evaluate the genetic composition of 884 individuals from 20 rivers. Bayesian clustering methods inferred groupings that were generally consistent with spatial distribution of rivers. A cluster in northeastern PEI was the most distinct, clustering separately across all methods. Distance between rivers accounted for 25.8% of the variations, whereas stocking intensity did not predict genetic variation. The genetic composition of the most heavily stocked river changed over a few years, suggesting that wild free-ranging fish could outcompete stocked fish. Currently, PEI has multiple genetic stocks that are consistent with the post-glacial biogeography rather than stocking history. Clarification of these adaptations is required to guide the incorporation of genetics into management strategies for the benefit of Atlantic salmon conservation.