The efficiency of three strategies carried out by fisheries managers to restore native Mediterranean brown trout populations threatened by non-native Atlantic populations were assessed. The strategies tested were (i) genetic refuge area where stocking is banned, (ii) stocking with Mediterranean fry and (iii) translocation of wild Mediterranean spawners. Using two discriminatory microsatellite loci between Atlantic and Mediterranean alleles, we compared the genetic composition of samples before and after the changes of practices. The three strategies had several detectable effects in the standing populations causing strong temporal changes in departures from Hardy–Weinberg equilibrium and linkage equilibrium between loci and the apparition of new Mediterranean alleles. The significant reductions in the proportions of Atlantic alleles observed over time can mostly be explained by the disappearing of the pure non-native Atlantic trout after the stopping of hatchery releases. The results, however, also suggest that the active strategies carried out by managers led to intraspecific introgression between both non-native Atlantic and native Mediterranean strains.