Spleen samples from 292 wild carnivores from Colorado, US were screened for Bartonella infection. Bartonella DNA was detected in coyotes (Canis latrans) (28%), striped skunks (Mephitis mephitis) (23%), red foxes (Vulpes vulpes) (27%), and raccoons (Procyon lotor) (8%) but not in black bears (Ursus americanus), gray foxes (Urocyon cinereoargenteus), and mountain lions (Puma concolor). Two Bartonella species, B. vinsonii subsp. berkhoffii and B. rochalimae, were identified. All 10 infected striped skunks exclusively carried B. rochalimae while coyotes, red foxes, and raccoons could be infected with both Bartonella species. Five of seven infected coyotes carried B. v. berkhoffii whereas five of seven infected red foxes and 11 of 14 infected raccoons carried B. rochalimae. Further studies are needed to understand relationships between Bartonella species, wild carnivores, and their ectoparasites.