We studied den use and den-habitat selection by the Prince of Wales Island flying squirrel (Glaucomys sabrinus griseifrons) at multiple spatial scales in fragmented temperate rain-forest habitats because of the role dens play in the distribution, reproduction, and population density of this endemic subspecies. We observed differences in spatial patterns associated with den use between juveniles and adults: juvenile core denning areas were almost an order of magnitude larger than those of adults, and juveniles used about one-half the number of dens per month as adults. Female juveniles exhibited both the largest mean and maximum movements between consecutive dens among all age and sex classes. At the microhabitat scale of den selection snags were not selected over live trees, but flying squirrels primarily used cavities in snags and live trees. Flying squirrels also selected dens in the largest diameter live trees and snags, in snags with intermediate levels of decay, in live trees with more conks and visible bole entries, and in western hemlock (Tsuga heterophylla). At the broader scale of den selection flying squirrels chose den locations in neighborhoods with higher-volume forests and lower levels of fragmentation, although not lower absolute amounts of edge, than was available across the landscape. Our results suggest that extensive modification of landscapes from clear-cut logging and the creation of an early-seral matrix appeared to influence spatial patterns of den use in flying squirrels and den selection at the broader scale. When compared to patterns in a more-intact landscape, den selection at the microhabitat scale did not relate to differences in landscape context, suggesting additional factors might play an important role in den use across the region.