Determining habitat associations of small mammal species and environmental characteristics important for site occupancy are central to understanding species biology and community organization. Most studies of small mammal communities are done at a local scale and in 1 habitat, overlooking patterns manifest over a heterogeneous landscape. During the summers of 2009 and 2010 we trapped small mammals throughout Wisconsin at 180 sites among 13 natural habitats, capturing 3,261 individuals of 23 taxa. We modeled site occupancy using habitat characteristics for 16 taxa while incorporating imperfect detection and compared small mammal community similarity among habitats. Site variation in tree density, soil moisture regimes, and winter temperatures were the most important variables in describing occupancy of species. With the exception of Zapus hudsonius and Sorex hoyi, occupancy rates of species were not the same across habitats. Species-specific responses to habitat characteristics created distinct natural habitat associations leading to unique and predictable small mammal assemblages. This study demonstrates the importance of sampling across a wide range of environmental gradients and habitats when determining the distribution of species and how communities are organized at a landscape level.