With the globally increasing trend towards urbanization, we need to understand how the subsequent host and ecological changes affect parasite communities. This study utilized an urban-natural gradient to detect differences in parasite assemblages within mice and voles in natural, rural, and urban sites. Prevalence and intensity levels of ectoparasites and intestinal helminths were estimated for two species of rodents, the Large Japanese field mouse (Apodemus speciosus) and the Grey red-backed vole (Myodes rufocanus) in the Tokachi region, Hokkaido. We predicted that parasite diversity will decrease toward urban areas, while prevalence and intensity of each species will be affected by their complex life history strategies, leading to complex patterns. This is the first intensive study utilizing rodents along an Urban-Natural gradient, and one of the few studies among all taxon to estimate helminth intensity levels. While most related studies are limited to a few species of parasites and lack a clearly defined sampling regime, we attempted to apply a more broad scale and methodical approach. We obtained 5 types of ectoparasites and 4 classes of helminths (Cestoda, Trematoda, Nematoda, Acanthocephala). While prevalence, intensity and diversity varied considerably among local habitats, the broad scale trend across the gradient is not so apparent.