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The Mediterranean brown trout (Salmo trutta complex) is one of the freshwater fish species complex at greater risk of extinction in the Mediterranean area. The introduction of alien invasive species and their interaction with the native fauna represent some of the major threats to the survival of this species. Currently, the genetic variability of the Mediterranean trout (Salmo trutta complex) is being compromised by the introgressive hybridization with the Atlantic trout (Salmo trutta Linnaeus, 1758). Therefore, it is necessary to gain further knowledge on genetic and demographic characteristics of Mediterranean trout populations, that, combined with environmental and angling data, will allow to undertake sound conservation strategies. The aims of the present study were to analyze: i) the demographic characteristics of the Mediterranean trout in seven central Apennine river basins where native populations are threatened by stocking with the domestic trout of north Atlantic origin; ii) the influence of both environmental parameters and different fishery management strategies on the status of native trout populations. The project focuses on 14 sites included in the Natura 2000 EU wide network of nature protection areas, established under the 1992 Habitat Directive. A total of 25 watercourses were investigated for a total of 32 sampling sites. A census of the fish fauna was carried out by electrofishing at each sampling location. Fish and environmental data were collected in spring and autumn 2014. The results obtained in the present research allowed us to detect the presence of three residual Mediterranean trout populations with a high degree of genetic integrity in the study area. The native trout populations were characterized by higher abundances and higher adult density values. Well-structured native populations with higher legal-size specimens density and poor body conditions in terms of relative weight were observed in the no-fishing areas, probably due to the presence of intraspecific competition phenomena. The environmental analysis confirmed the key role played by the geological characteristics of the central Apennines in shaping the introgression levels observed in the wild trout populations, while the recovery of the water quality appears decisive in the development of management strategies aimed at their conservation.