Patterns of genetic variation of a species can be shaped by events that occur at wide temporal and geographic scales. Geophysical processes, such as continental glaciations, can affect species vicariance at wide scales whereas processes that act at finer scales, such as gene flow between populations, can have more localized effects. Recent studies have shown that contemporary population structure should be interpreted within the context of historical events, such as ice-age vicariance, due to the hierarchical nature of genetic variation found in many species. The thinhorn sheep (Ovis dalli) is a mountain specialist found in northwestern North America, from the Brooks Range in Alaska, east through Yukon to the Mackenzie Mountains of Northwest Territories and south to the Rocky and Coastal Mountains of British Columbia. In this study, we examined the population genetic structure of thinhorn sheep in light of genetic evidence regarding the glacier driven evolution of the two thinhorn sheep subspecies, O. d. dalli and O. d. stonei, using 153 biallelic single-nucleotide polymorphisms genotyped in over 2800 thinhorn rams. We found patterns of genetic variation to be generally consistent with genetic subspecies boundaries at the species-wide level, and mountain range and river valley boundaries at finer scales. By taking in account historical vicariance by conducting hierarchical analyses of population genetic structure, we revealed the presence of three previously unreported Stone’s sheep genetic clusters in the Stikine/Skeena, Cassiar and Rocky Mountains and identified a new geographic range for Stone’s sheep that is much more restricted than currently accepted subspecies maps indicate, and is almost exclusively confined within British Columbia. Our results indicate that contemporary patterns of genetic variation can be influenced by events acting over a range of spatial and temporal scales, and thus the importance of interpreting the findings of present-day genetic structure in light of the phylogeographical history of the species in question.