Two species of mice, the white-footed mouse, Peromyscus leucopus (Rafinesque; Rodentia: Cricetidae) and the woodland deer mouse, Peromyscus maniculatus (Wagner; Rodentia: Cricetidae), serve as reservoirs of tick-borne pathogens in many parts of North America. However, the role P. maniculatus plays in the amplification and maintenance of Anaplasma phagocytophilum (Rickettsiales: Ehrlichiaceae) and Borrelia burgdorferi (Spirochaetales: Spirochaetaceae) is not well understood. In northern Wisconsin, from 2012 to 2014, 560 unique mice were captured at 83 sites distributed across five forests. P. leucopus was more likely infested with immature Ixodes scapularis compared to P. maniculatus (60.1 vs. 28.3%). Abundance of immature I. scapularis on P. leucopus (M = 2.69; SD = 3.53) was surprisingly low and even lower for P. maniculatus (M = 0.717; SD = 1.44). Both P. leucopus and P. maniculatus were infected with B. burgdorferi, 24.0 and 16.8%, respectively. The prevalence of A. phagocytophilum infection in P. leucopus (1.69%) was similar to that observed in P. maniculatus (4.73%). Nine of 10 mice co-infected with both pathogens were P. maniculatus, and there were more co-infections in this species than expected by chance (3.07 vs. 0.82%). Differences in the behavior and biology between these two mice species may contribute to the variation observed in the abundance of host-attached ticks and pathogen prevalence. These differences highlight a potential hazard of the failure to differentiate between these visually similar mice, but there is evidence that these two mice species can each serve as reservoirs for tick-borne pathogens that cause human disease in Wisconsin.