Effective management strategies require an understanding of the spatial scale at which fauna use their habitat. Toward this end, we sampled small mammals in the northern Sierra Nevada, California, over 2 years at 18 livetrapping grids among 5 forest types. Forest types were defined by overstory tree composition, and 19 microhabitat variables were measured at all trap stations. Forest type and year explained 93% of variation in abundance of North American deermice (Peromyscus maniculatus), whereas only 40% was explained by microhabitat and year. Similarly, variation in abundance of long-eared and shadow chipmunks (Neotamias quadrimaculatus and N. senex) was better explained by forest type and year (67%) than by microhabitat and year (30%). Red fir (Abies magnifica) forests supported more P. maniculatus and Neotamias species than mixed-conifer and pine–cedar forests, and more Neotamias species than mixed-fir forests. Five of 6 uncommon species were significantly associated with forest type; golden-mantled ground squirrels (Spermophilus lateralis), northern flying squirrels (Glaucomys sabrinus), and long-tailed and montane voles (Microtus longicaudus and M. montanus) were captured almost exclusively in red fir forests, whereas dusky-footed woodrats (Neotoma fuscipes) and California ground squirrels (Spermophilus beecheyi) were found in pine–cedar, mixed-fir, and mixed-conifer forests. The first 2 axes of a canonical correspondence analysis on microhabitat variables explained 71% of variation in combined small mammal abundance. Microhabitat associations varied among species but were driven primarily by canopy openness, shrub cover, and shrub richness. Although much of the small mammal fauna appeared to select habitat at both spatial scales studied, canonical correspondence analysis using forest type as a covariate revealed that microhabitat explained much less variation in small mammal abundance than did forest type.