Microsatellite analysis of Atlantic salmon from five Danish rivers was performed to determine the stocked or indigenous status of individuals. Genetic variation at six highly polymorphic microsatellite loci was assayed and used for individual based analyses (assignment tests). Contemporary samples of adult returning spawners and fry were compared to baseline data from: 1) historical DNA samples (from old scales) representing the indigenous populations, 2) samples from another Danish population (Skjern River) used for stocking, and 3) five exogenous populations used for stocking. Assignment power was high. The percent of stocked salmon correctly assigned to population of origin ranged from 83% to 99% and the percent of indigenous salmon correctly assigned to population of origin ranged from 83% to 90%. For two of the rivers significantly more individuals were assigned to the indigenous populations than expected from misclassification alone, suggesting that some remains of the indigenous populations had persisted. Still, many fish were of exogenous origin. Simulated hybrids among released exogenous salmon and between exogenous and released Danish salmon (Skjern River) revealed that natural hybridisation among released fish was not likely to be the source of the fry classified as indigenous, however, the possibility of hybridisation among indigenous and released fish could not be dismissed. Several full sib groups were found among indigenous natural fry ruling out one or a few matings as the source of the indigenous fry. These results show that some native populations may persist even after years of introduction and environmental perturbation; genetic information can be used to identify these populations and identify individuals representing these populations for use in re..