Abstract – Investigating the influence of evolutionary forces on the genetic structure and genetic diversity remains a major challenge. Yet, it is of considerable interest for conservation and management of a species. This study investigates the influence of life-history and landscape features, such as altitude, connectivity and habitat size, on genetic diversity and genetic structure of brown trout (Salmo trutta L.) with stream-resident, lake-dwelling and sea-migrating life-history in two river systems in northern Sweden. Using regression tree analysis including ecological and landscape characteristics, we show that life history is the most important variable explaining genetic diversity and population differentiation. Sea-migrating populations show high diversity and low differentiation, and lake- and stream-resident populations show low diversity and high population differentiation, among all samples. No overall genetic correlation with geographical distance was noted; however, among sea-migrating populations within the River Vindelälven drainage, this pattern was observed. This study illustrates that life-history and landscape features help to explain genetic structure and genetic variation. The information is important for conservation and management actions, such as fisheries regulations, habitat restorations, stocking of hatchery fish, defining management units and introducing genetic monitoring programmes.