Over the last 50 years, populations of Cantabrian Atlantic salmon (Salmo solar) have been in decline. In response to the declines, restocking of the rivers using non-native eggs and juveniles was carried out; the restocking activities may have been responsible for introductions of infectious diseases, this thesis examines the genetic effects on the Cantabrian Atlantic salmon populations of population decline, stocking and infectious disease using a mtDNA gene, 13 neutral nuclear microsatellites and three functional gene markers. In addition to the population genetic findings, evidence for possible interspecific mitochondrial recombination was discovered. Despite the population decline, little evidence for erosion of genetic variability at any marker class was observed.