Atlantic salmon Salmo salar supports highly valuable commercial and recreational fisheries in Europe, but its stocks are currently overexploited and threatened by climate change. Its southernmost populations (in northern Spain) play a key role in conserving the species’ original genetic diversity, which is endangered due to decades-long (1970s to 1990s) massive stocking with non-native stocks. Their decline is well documented, but the effect of stock transfer and conservation efforts is unclear. Nine microsatellite loci were amplified from archival samples (scales from 1958–1959) from eight Spanish rivers to analyse the species’ natural genetic dynamics before its decline started. Allelic richness was high in the historical populations (the 1950s) and above most contemporary estimates. Private alleles were found in most rivers, indicating high local uniqueness and relative isolation among river basins. Some alleles are regional markers since they are rare or absent from contemporary northern European populations. Effective population size suggested good conservation status, with higher values than those estimated for contemporary populations. Strong population structure and genetic differentiation between rivers were found, with limited gene flow, restricted to geographically close populations. Our estimates of historical genetic diversity and structure from southernmost salmon populations are a powerful benchmark to guide conservation programs.
