Many animals undertaking long-distance migrations use Earth’s magnetic field as a “map” to assess their position for orientation. This phenomenon been particularly well-studied in salmonids using “magnetic displacement” experiments, in which animals are presented with magnetic field conditions that are characteristic of other geographic locations. However, whether use of magnetic map cues differs among populations of salmon has not been investigated. Here we show that nonanadromous and anadromous populations of Atlantic salmon (Salmo salar) raised under the same conditions within their native range differ in their response to magnetic displacements in the North Atlantic. The directions adopted by anadromous salmon juveniles to each of the magnetic displacements would support their migration from the eastern US to western Greenland, had the fish actually been at those locations. In contrast, nonanadromous salmon did not appear to respond to the magnetic displacements. The findings are consistent with the hypothesis that the innate magnetic map of anadromous salmon is adapted to guide their marine migration.