Urocitellus brunneus (northern Idaho ground squirrel) has a geographic range of approximately 1,600 km² in west-central Idaho. It was listed as Threatened under the US Endangered Species Act in 2000. To assist recovery efforts, we tested three hypotheses that might explain its rarity: 1) specialization on a now uncommon habitat; 2) competition with a larger congener, U. columbianus (Columbian ground squirrel); and 3) anthropogenic impacts. We explored the habitat specialization hypothesis by comparing attributes of sites occupied exclusively by each species with areas occupied alternately by each. Sites occupied by U. brunneus had significantly more bare ground; shallower, rockier, harder soils; higher soil temperatures during the active season; less plant cover; shorter vegetation; lower net annual aboveground productivity; and fewer shrubs than sites occupied by U. columbianus. Discriminant analysis showed U. brunneus could occupy some areas used by U. columbianus, but U. columbianus seldom occupied areas occupied by U. brunneus. U. brunneus also occurred in earlier successional communities and could occupy mesic meadows with high water tables not utilized by U. columbianus. In field observations and arena trials, U. brunneus avoided U. columbianus. In two removal experiments U. brunneus expanded into areas from which U. columbianus had been removed, but vacated when U. columbianus returned. Anthropogenic impacts included habitat conversion, conifer invasion of meadows resulting from timber management and fire suppression practices, systematic poisoning, target shooting, and invasive species; grazing appears to have mixed impacts. U. brunneus is rare due to a combination of habitat specialization, competition, and anthropogenic impacts.