Species that inhabit fragmented habitats are expected to exhibit spatial genetic structure with respect to geographic distance and landscape features. These patterns are also shaped by a variety of temporal processes, namely post-glacial recolonization, and those operating at more contemporary scales, such as sex-biased dispersal. We quantified the spatial population genetic structure of mountain goats (Oreamnos americanus) in northern British Columbia (BC). We observed little genetic differentiation among mountain ranges across northern BC, suggesting a panmictic subpopulation. Genetic diversity values increased slightly with latitude, while bottleneck signatures were strongest in the south; these signatures are indicative of southward post-glacial colonization consistent with a northern glacial refugium. Mountain ranges were the most important predictor of genetic relatedness, suggesting large valleys impeded gene flow, and specific landscape features were not correlated to genetic variation. We used a case study in the Skeena region of BC to show how these data can directly inform local management recommendations. This study provides insight and much needed clarification of the genetic population structure of North American mountain goats and illustrates the limited impact of geographic distance and landscape features on gene flow in the northern half of the range.