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. To better understand the evolutionary and demographic consequences of these historical events, this project will analyze a large collection of whole-genome sequences from harbor seals sampled across the Skagerrak and Kattegat. By leveraging extensive genome-wide variation from individuals representing multiple regions of the metapopulation, we will characterize patterns of genetic structure, connectivity, and diversity at unprecedented resolution. This comprehensive genomic dataset will also enable us to investigate signatures of selection and identify genomic evidence of differential exposure and responses to past disease outbreaks, providing insights that are essential for understanding the resilience of the Swedish–Danish harbor seal metapopulation and informing its future conservation and management.