The level of introgression between wild and stocked individuals in Portuguese brown trout Salmo trutta L. populations was evaluated. Fish were sampled from rivers of the Douro Basin and compared with fish used in restocking programme. This study, based on microsatellite and allozyme loci, showed, thanks to the most discriminant loci, a low percentage of heterozygote individuals. This happened due to absence or low levels of intercrossing between stocked and native brown trouts. It was confirmed the inefficiency of stocking practices in Portugal, as suggested by mtDNA haplotype distribution. From the management and conservation points of view, any kind of stocking with exogenous specimens should be avoided to allow preservation of the autochthonous genetic pools. As well as the stocking techniques and released fish density should be considered. Therefore new policies for stocking and monitoring hatchery fish are needed to preserve the gene pools of wild Portuguese trout populations.