The genetic effects on Atlantic salmon, Salmo salar L., populations from potential bottleneck situations caused by human activities in two Norwegian rivers, Lærdalselva and Batnfjordelva, were studied by analysing DNA from fish scales collected before and after the populations had been exposed to human-induced changes: river regulation, Gyrodactylus salaris infection and rotenone treatment. Using 15 microsatellites, no significant changes were found in the genetic structure and diversity of four population samples from Lærdalselva collected over 34 years. However, salmon from Lærdalselva were significantly differentiated from nearby (Årøyelva) and more distant (Batnfjordelva and Suldalslågen) populations, testifying to the power of the marker system to detect small genetic differences. Furthermore, two population samples from Batnfjordelva, collected 20 years apart, showed low but significant differentiation. The lack of effects on neutral genetic composition in Lærdalselva, despite several potentially severe bottleneck events, indicates that stocking and sea cohorts maintain the status quo of this population.