The relationships between populations of the Deer Mouse (Peromyscus maniculatus) and the White-footed Mouse (P. leucopus) and their respectiveCuterebraparasites were examined. Population genetic structure of hosts and parasites was inferred using cytochrome oxidase mitochondrial sequences of specimens from 7 populations. Genetic analyses revealed that isolation-by-distance applies forP. maniculatusand its associated parasite (C. grisea). A significant correlation was also observed between the genetic distances of these host and parasite species. Furthermore, populations ofP. maniculatusandC. griseafrom the North and South shores of the St Lawrence River were found to be significantly different. This structure may be explained by the St Lawrence River being a dispersal barrier for both species. A robust analysis of the other species pair (P. leucopusandC. fontinella) could not be performed because of limited sample sizes.