Babesia are intraerythrocytic protozoans, many of which have veterinary/medical importance. Two morphologically similar species, Babesia lotori and Babesia microti-like sp., occur in raccoons (Procyon lotor). Little is known of the distribution and prevalence of these parasites and recently maned wolves (Chrysocyon brachyurus) in a Missouri zoo have been diagnosed with severe/fatal babesiosis caused by B. lotori. Raccoon blood and spleen samples were obtained from locations in the USA and Canada and tested using species-specific PCR assays. B. lotori prevalence was highest in the Southeast (20-45% [142/519]) and B. microti-like sp. was detected at all sites with general prevalence highest in the Southeast (67-100% [382/519]). Coinfections were common. For neonate raccoons, 62% (66/106) were positive for B. microti-like sp., 10% (11/106) for B. sensu stricto, and 7.5% (8/106) were co-infected. Currently transmission route is unknown for both Babesia spp., thus these data may assist in determining potential vector(s).