Identifying the differences in ecology between closely related species occupying the same environment contributes to our understanding of community diversity, ecosystem structure, and species conservation. Endemic Bear Lake whitefish (Prosopium abyssicola) and Bonneville whitefish (Prosopium spilonotus) are benthic, morphologically similar, and closely related, yet the extent of differential resource use remains poorly understood. To determine the ecological differences between these two species, we studied their seasonal distribution and diet in Bear Lake, Utah–Idaho. We used bottom-set gill nets to examine how catch of each species of whitefish varied in relation to depth and season (spring and summer). In both spring and summer, Bonneville whitefish dominated the shallower depths (5–30 m), whereas Bear Lake whitefish dominated the deeper depths (45–55 m). Bonneville whitefish ate a variety of benthic invertebrates, but mostly Chironomidae, whereas Bear Lake whitefish fed mostly on Ostracoda. These data describe a closely related morphologically similar, yet ecologically distinct group of whitefish in an ecoregion completely different from those studied before. These results indicated that each species has a very different role in the Bear Lake ecosystem. To conserve this unique fish assemblage, both shallow and deepwater habitats need to be protected.