The Mediterranean brown trout (Salmo trutta species complex) comprises genetically and ecologically distinct lineages primarily distributed across the Western Mediterranean region. Conservation of the Mediterranean brown trout is complicated by unresolved taxonomy. Although some populations have recently been recognised as distinct species, most—including those in the Iberian Peninsula—remain classified under the nominal S. trutta, which is currently listed as Least Concern by the IUCN. This taxonomic ambiguity masks severe conservation threats, particularly the widespread genetic introgression from stocked Atlantic-origin trout. In this study, we assessed introgression patterns, environmental drivers and conservation implications for Mediterranean brown trout populations in Catalonia (northeastern Iberian Peninsula). Genetic data from 134 sites were analysed using microsatellite markers and LDH-C1* allele frequencies, and the influence of historical stocking intensity and climatic variables on introgression was evaluated using hierarchical partitioning and regression models. Our results revealed extensive introgression, with only 10.4% of the populations retaining genetic purity. Stocking intensity was the primary predictor of introgression, followed by temperature and precipitation seasonality. Although the overall distribution of brown trout in the region remains stable, genetically pure Mediterranean populations have experienced severe range contraction, with a 61.5% reduction in extent of occurrence (EOO) and an 89.6% reduction in area of occupancy (AOO). This decline might meet IUCN criterion B for Endangered, although a formal assessment is currently impeded by taxonomic uncertainty and data limitations. The recognition of Mediterranean brown trout as a distinct species, alongside urgent measures to halt ongoing introgression and preserve remaining pure populations, is essential for its long-term conservation.