Abstract Brown trout is a species complex ( Salmo trutta complex, L., 1758) including both widespread invasive (non‐native hatchery strains) lineages and endangered local‐endemic lineages, among which is the Sardinian trout, the only native salmonid present in Sardinia. Multiple stressors (e.g. the spread of stocked brown trout of Atlantic origin, habitat alteration and climate change) combine to seriously threaten the persistence of wild native populations. In this study, the origin, population genetics and demography of wild Sardinian brown trout populations were extensively investigated. A total of 274 trout individuals collected from 12 hydro‐geographical basins were analysed using both mitochondrial (control region) and nuclear ( LDH‐C1* locus and 10 microsatellites) markers. Although stocking activities have altered the native genetic makeup of some populations in the study area, several (almost) uncontaminated populations showing strong genetic structure were detected. Eroded intra‐population diversity, as well as small effective population size, sometimes associated with a bottleneck signal was also found. The genetic characteristics of Sardinian trout populations described in this study are probably due, at least partly, to the peculiarity of local environmental conditions at the margin of the ecological niche for salmonids. Based on the results of this study, the need for urgent measures of conservation aimed to ensure the near future viability of the last wild Sardinian trout populations was discussed.