The presence of keystone species can influence disease dynamics through changes in species diversity and composition of vector and host communities. In this study, we compared 1) the diversity of small mammals; 2) the prevalence, abundance, and intensity of arthropod vectors; and 3) the prevalence of Yersinia pestis, Francisella tularensis, and Bartonella spp. in vectors, between two grassland communities of northern Sonora, Mexico, one with (La Mesa [LM]) and one without (Los Fresnos [LF]) black-tailed prairie dogs (Cynomys ludovicianus). The mammal community in LF exhibited higher species richness and diversity than LM, and species composition was different between the two communities. Flea species richness, prevalence, abundance, and intensity, were higher in LM than in LF. The most abundant fleas were Oropsylla hirsuta and Pulex simulans, and C. ludovicianus was the host with the highest flea intensity and richness. There was no serologic evidence for the presence of Y. pestis and F. tularensis in any community, but Bartonella spp. was present in 18% of the total samples. Some specificity was observed between Bartonella species, flea species, and mammal species. Although prairie dogs can indirectly affect the diversity and abundance of hosts and vectors, dynamics of vector-borne diseases at these spatial and temporal scales may be more dependent on the vector and pathogen specificity.