The risks of supplementation must be examined to assess the genetic effects to native wild populations before full implementation or exclusion of programs that involve captive breeding and release. Real genetic data can be applied to simulations of genetic changes in populations of interest and subsequently used in risk assessment. Ancestral Mediterranean brown trout (Salmo trutta) lineages exhibit complex population structure among native populations. Genetically divergent Atlantic stocks were maintained and released in the Mediterranean rivers as recreational fish, which resulted in hybridization and introgression with local populations. Therefore, we designed a new supplementation program based on native stocks and evaluated the genetic risks associated with releasing native fish in recreational fisheries. Our simulation was delimited by the observed population genetic structure and available hatchery facilities in the study region. Supplementation with native stocks maintained estimates of gene diversity indexes (total diversity (HT), local diversity (HS), and population differentiation (GST)). However, simulations indicated that long-term supplementation significantly reduced genetic diversity among locations because of a homogenizing effect of populations along each management unit. Therefore, such reinforcements compromised the conservation of local genetic variation. Nevertheless, replacement of current foreign stocks with native stocks can be an important step towards promoting the value of preserving local diversity among anglers.