Here, we used genomic approaches to study the population structure, genetic diversity, evolutionary history and local adaptation of North Atlantic Harbour porpoises (Phocoena phocoena). Our results shed light on the expansion of harbour porpoise populations across the North Atlantic, demonstrate that genome-wide data can unravel subtle population structure and contribute to understand how marine species adapt to their local environment. The results have great conservation implications as we found major levels of inbreeding and low genetic diversity in the endangered Black Sea subspecies and identified the critically endangered Proper Baltic Sea porpoises as a separate population.