Genetic evidence for the selective exploitation by anglers of early running fish was examined in four Iberian Atlantic salmon populations using protein and mtDNA markers. The populations studied had been exploited exclusively by anglers since 1949 during a fixed fishing season that ran approximately from March to July. Genetic variation at six protein loci was small and was accounted for by the MEP-2* and MDH-3,4* polymorphisms, which generally remained stable over time and were in Castle–Hardy–Weinberg equilibrium during the fishing season. Early running fish that had spent multiple winters at sea (MSW) generally had higher frequencies of the common MEP-2*(100) allele than did late running, one sea winter (1SW) grilse that were significantly smaller and tended to escape the fishery. Spawners differed from angler caught fish in their mtDNA frequencies and consistently had a lower sea-age and a smaller body size. Spawners also smolted at an older age and displayed lower frequencies of the MEP-2*(100) allele in three of the four populations studied. These results suggest that in these rivers anglers selectively exploit a distinct component of the population and inadvertently cause a differential mortality of genetic types that is likely to be detrimental to population viability.