Loss of genetic diversity is a critical threat to biodiversity because it reduces the capacity of populations to survive and adapt to rapid environmental change. Pilot programs for monitoring of genetic diversity for conservation management are in progress in a few countries and different approaches are being applied and evaluated. Here, we explore the potential to monitor genome wide genetic changes over contemporary time frames using whole genome sequencing (WGS) of pools of individual DNA (Pool-seq). We study populations of brown trout (Salmo trutta) in alpine lakes in protected areas of central Sweden and explore changes over a 40-year period (ca. 6 trout generations).