Agriculture and development have dramatically reduced the range of native bunchgrass habitats in the Northern Rocky Mountains, and the invasion of exotic plants threatens to greatly alter the remaining pristine prairie. Small mammals play many important roles in ecosystem functions, but little is known about small mammal community composition and structure in native bunchgrass habitats of the Northern Rocky Mountains. We live trapped small mammals along transects to study community composition, relative abundance, and habitat relationships in three native bunchgrass sites (Bandy Ranch, Sieben Ranch and Wildhorse Island) of west-central Montana, USA. All sites fall into the rough fescue/Idaho fescue (Festuca idahoensis) habitat types, but dominant grasses varied at microsites among rough fescue, Idaho fescue and bluebunch wheat grass (Agropyron spicatum [Elymus spicatus]). Small mammal community composition and relative abundance were consistent among sites, with deer mice (Peromyscus maniculatus) dominating, followed by montane voles (Microtus montanus), which were uncommon, and montane shrews (Sorex monticolus), which were rare. Deer mice and montane voles exhibited complementary habitat separation. Deer mice tended to select open microsites and avoid sites with high percentages of vegetative cover. Male and female deer mice demonstrated strong habitat separation at two sites, but the habitat variables partitioned between sexes differed by site. Montane voles avoided open sites and selected for concave microsites where the vegetative cover was relatively dense. This information provides an important baseline for understanding pre-settlement small mammal communities in the rapidly dwindling, native bunchgrass habitats of the Northern Rocky Mountains.