Hibernation is a strategy many species employ to survive periods of thermal stress or resource shortage (e.g., harsh thermal conditions, food limitations) and habitat requirements of hibernating species may differ between summer (the active season) and winter (during hibernation). Accounting for seasonal differences in habitat affinities will help ensure that management actions are more beneficial and land-use policies are more appropriate. The northern Idaho ground squirrel (Urocitellus brunneus) is a federally listed threatened species that is in decline and hibernates for approximately 8 months per year. We collared northern Idaho ground squirrels in Adams County, Idaho from 2013–2017. The majority of northern Idaho ground squirrels we collared selected hibernacula outside of the areas they used during the active season. Furthermore, habitat features of hibernacula locations differed from habitat features of active-season areas. Hibernacula locations had greater canopy closure compared to active-season locations (36.9% and 7.0% canopy closure, respectively) and hibernaculum habitat features (particularly distance to nearest log) influenced overwinter survival. Our results suggest that recovery efforts for northern Idaho ground squirrels should include protection and management for the full range of habitat conditions used throughout summer and winter. More broadly, we emphasize the need to identify and protect habitat during all seasons because habitat requirements can differ substantially during different portions of an animal's annual cycle and effective conservation will require management of year-round habitat needs.