Dusky-footed woodrats (Neotoma fuscipes) are important components of forest communities, including serving as a primary prey of the California spotted owl (Strix occidentalis occidentalis), a species of concern in California. We examined habitat associations of the dusky-footed woodrat at 4 study sites in mixed-conifer forest of the northern Sierra Nevada, California, during 2003–2005. We investigated the importance of California black oak (Quercus kelloggii) as a macrohabitat component for woodrats, and we examined microhabitat association at 2 levels, house location and house use, by comparing house-site (n = 144) characteristics to random sites (n = 144) and characteristics of used and unused houses, respectively. Woodrat density was positively related to density of large (≥33-cm-diameter at breast height) oaks, probably because large oaks are valuable food resources. Location of woodrat houses was strongly influenced by the presence of large (≥30-cm-mean diameter) logs and large (≥30-cm-diameter at root collar) stumps, but also by steeper slopes, and lack of bare ground and mat-forming shrub cover. We found little evidence that adult woodrats distinguished among houses with respect to microhabitat, suggesting that woodrats make decisions about microhabitat suitability when the house is built. In 2005, adults chose larger houses that were characterized by more logs and less poletimber than those of subadults, but we detected no such differences in 2004. Dusky-footed woodrats in the northern Sierra Nevada would benefit from management techniques that promote the growth and retention of large California black oaks and create large logs and stumps within a stand.