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The harbour seal Phoca vitulina is a marine mammal predator with potentially significant ecological impacts. Two subspecies exist in North America, P. v. richardii in the Pacific Ocean, and P. v. concolor in the Atlantic. Across the coastal ranges of the harbour seal, strong natal philopatry results in fine-scale genetic structure and isolation-by-distance. A stepwise decrease in genetic diversity in the subspecies was recently reported, with highest diversity in the eastern Pacific Ocean, medium diversity in the western Atlantic Ocean, and lowest diversity in the eastern Atlantic Ocean. Management of harbour seals is expected to benefit from improved resolution of fine-scale population structure and dynamics. Here we use genotyping-by-sequencing to genotype 146 harbour seals from the eastern Pacific Ocean (i.e., British Columbia, Oregon, and California) and the western Atlantic Ocean (i.e., Québec, Newfoundland, and Labrador). Using 12,742 identified variants, we confirm elevated genetic diversity in the eastern Pacific, and determine that this is independent of reference genome bias or other potential technical artefacts. The largest differentiation occurs between the subspecies, followed by divergence between British Columbia and Oregon-California, and between Québec and Newfoundland-Labrador. Gradual separation in samples and lower differentiation is viewed between California and Oregon, and between northern and southern BC. Unexpected outlier clusters were observed in two populations due to cryptic relatedness of individuals, which were subsequently removed from the analysis. Additional sampling is needed in the central and north coast of British Columbia to determine whether a discrete separation of populations exists within the region.