Understanding habitat use by remnant populations of imperiled species can inform conservation efforts. Arctic ground squirrels (AGS; Urocitellus parryii) occupy alpine and boreal forest habitats in southwestern Yukon, Canada, where populations have been monitored since the 1970s. While alpine populations have remained stable, those in the boreal forest collapsed in the late 1990s and have not recovered. Propelled by the region-wide decline of AGS at low-elevation sites, our purpose was to document site occupancy by remnant populations and to identify habitats that are a high priority for monitoring and have potential for conservation. Using walking transects, we surveyed 155 sites in eight study areas for presence of AGS. Model-averaged occupancy probability was 0.643 (SE = 0.066), and the associated detection probability was 0.835 (SE = 0.075). AGS occurrence was strongly related to increasing habitat openness and also positively influenced by anthropogenic habitat and neighborhood occupancy. The availability of open habitat patches and connectivity among colonies within the boreal forest are consequential for the persistence of low-elevation populations of AGS. These factors may be linked to predator avoidance. Shrubification in the boreal forest as a result of climate warming may reduce AGS ability to detect and avoid predators. Recognizing anthropogenic habitats in land-use planning, and managing potential conflicts with landowners, may be important for the persistence and recovery of AGS at the southern edge of their range.