Author Summary Plague, a severe and often fatal zoonotic disease, is caused by the bacterium Yersinia pestis. Currently, the majority of human cases have been reported from resource limited areas of Africa, where the proximity to commensal rats and other small mammals increases the likelihood for human contact with infected animals or their fleas. Over a 9 year time period, >1000 suspect cases were recorded in the West Nile region of Uganda within the districts of Arua and Zombo. Culture-confirmed cases were shown by three independent typing methods to be due to two distinct 1.ANT genetic subpopulations of Y. pestis. The two genetic subpopulations persisted throughout the 9 year time period, consistent with their ongoing maintenance in local enzootic cycles. Additionally, the two subpopulations were found to differ with respect to geographic location and elevation, with SNP Group 1 strains being found further north and at lower elevations as compared to SNP Group 2. The relative independence of the two Y. pestis subpopulations is suggestive of their maintenance in distinct foci involving enzootic cycles with differing vector-host community composition.