Conservation strategies that rely on umbrella species depend on spatial overlap with target species of concern, yet the temporal and spatial scale at which co-occurrence is assessed is rarely considered. In seasonal environments, shifts in space use across seasons could alter patterns of co-occurrence, especially at regional and local scales that are relevant to land management. Greater sage-grouse (Centrocercus urophasianus), which currently serve as an umbrella species for sagebrush ecosystems across the western United States, move between seasonal habitats. Our goal was to evaluate the degree to which sage-grouse general and seasonal habitats overlap with habitat for another sagebrush-dependent species of conservation concern, the pygmy rabbit (Brachylagus idahoensis). We created inductive species distribution models for both species in east-central Idaho. We used maximum entropy methods to build models incorporating environmental factors representing topography, vegetation, climate, and soil characteristics. Despite both species being sagebrush obligates, we documented a relatively modest degree of spatial overlap between these species across the region; only 49% of highly suitable habitat for pygmy rabbits overlapped with areas mapped as highly suitable for sage-grouse when considering general habitat, and overlap was lower (18–31%) when we evaluated seasonal sage-grouse distributions. Our models predicted that pygmy rabbits would also occur in narrow (1–2 km) sagebrush corridors between steep terrain features where sage-grouse are typically absent. This work suggests that additional habitat conservation for pygmy rabbits will be needed to support their long-term persistence, especially where their habitat falls outside of areas designated as primary habitat for sage-grouse. Our models provide useful information for land management and habitat restoration within the study region and also offer a cautionary tale for application of simplified conservation strategies like the designation of umbrella species. Incorporating spatial and temporal scales into assessments of co-occurrence may increase effectiveness of conservation strategies involving surrogate species.