Background: Anadromous migratory fish species such as Atlantic salmon (Salmo salar) have significant economic, cultural and ecological importance, but present a complex case for management and conservation due to the range of their migration. Atlantic salmon exist in rivers across the North Atlantic, returning to their river of birth with a high degree of accuracy; however, despite continuing efforts and improvements in in-river conservation, they are in steep decline across their range. Salmon from rivers across Europe migrate along similar routes, where they have, historically, been subject to commercial netting. This mixed stock exploitation has the potential to devastate weak and declining populations where they are exploited indiscriminately. Despite various tagging and marking studies, the effect of marine exploitation and the marine element of the salmon lifecycle in general, remain the "black-box" of salmon management. In a number of Pacific salmonid species and in several regions within the range of the Atlantic salmon, genetic stock identification and mixed stock analysis have been used successfully to quantify exploitation rates and identify the natal origins of fish outside their home waters - to date this has not been attempted for Atlantic salmon in the south of their European range.Results: To facilitate mixed stock analysis (MSA) of Atlantic salmon, we have produced a baseline of genetic data for salmon populations originating from the largest rivers from Spain to northern Scotland, a region in which declines have been particularly marked. Using 12 microsatellites, 3,730 individual fish from 57 river catchments have been genotyped. Detailed patterns of population genetic diversity of Atlantic salmon at a sub-continent-wide level have been evaluated, demonstrating the existence of regional genetic signatures. Critically, these appear to be independent of more commonly recognised terrestrial biogeographical and political boundaries, allowing reporting regions to be defined. The implications of these results on the accuracy of MSA are evaluated and indicate that the success of MSA is not uniform across the range studied; our findings indicate large differences in the relative accuracy of stock composition estimates and MSA apportioning across the geographical range of the study, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the area studied. This result probably reflects the more genetically distinct nature of populations in the database from Spain, northwest France and southern England. Genetic stock identification has been undertaken and validation of the baseline microsatellite dataset with rod-and-line and estuary net fisheries of known origin has produced realistic estimates of stock composition at a regional scale.Conclusions: This southern European database and supporting phylogeographic and mixed-stock analyses of net samples provide a unique tool for Atlantic salmon research and management, in both their natal rivers and the marine environment. However, the success of MSA is not uniform across the area studied, with large differences in the relative accuracy of stock composition estimates and MSA apportioning, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the region. More broadly, this study provides a basis for long-term salmon management across the region and confirms the value of this genetic approach for fisheries management of anadromous species.