Abstract: Multi-host pathogens are ubiquitous in natural environments and are often associated with emerging infectious diseases in humans, domesticated animals and wildlife; however, little is known concerning their community level dynamics in natural systems. A tractable system to study cross-species transmission of disease is to examine differences in infection rates of generalized and specialized parasites in allopatric and sympatric host communities. Allopatric and sympatric populations of Peromyscus leucopus and Peromyscus maniculatus were trapped in three locations across their shared geographic range. Intestinal parasites were identified to species and quantified from fecal samples to determine species richness, prevalence and intensity in each population type. Overall patterns of infection appeared similar between population types, although slight differences between species were consistently observed. Host community diversity of small mammals showed significant differences in prevalence, parasite richness and intensity of infection for nematodes and coccidians, with more specialized parasite prevalence decreasing with diversity. Results indicate that sympatric species of Peromyscus are infected with intestinal parasites in similar patterns and that host community diversity may play a role in patterns of infection by multi-host pathogens.