Globally, harbor seals span temperate and Arctic waters of the North Pacific and North Atlantic, including the Skagerrak and Kattegat regions, where they have been monitored since the late 1970s. After sharp declines from early-1900s hunting, protections in the 1960s–70s led to an exponential growth of the population, though PDV (phocine distemper virus) outbreaks in 1988 and 2002 resulted in the death of an estimated 65% of the population. Recent population surveys indicate that the Swedish-Danish metapopulation have increased until 2016 and seems to have plateaued out, with signs of declining pup production and slower growth. Because Swedish–Danish harbor seals have endured hunting, disease, and other pressures, studying their genetics is crucial for understanding how past environmental stress has shaped current metapopulation structure, resilience and management needs. Through the analysis of the genomes of individuals from different regions in the Skagerrak and Kattegat, we aim to shed light on the genetic structure of the Swedish-Danish harbor seal metapopulation and find genomic indications of differential exposure to disease outbreaks in the metapopulation.