Prescribed burning and mechanical thinning are used to manage fuels within many western North American forest ecosystems, but few studies have examined the relative impacts of these treatments on forest wildlife. We sampled northern flying squirrels (Glaucomys sabrinus) and microhabitat variables in burned, thinned and control stands of mixed-conifer forest of the southern Sierra Nevada at the Teakettle Experimental Forest. We used this information to determine the effects of burning and thinning on the microhabitat associations of flying squirrels. Across pretreatment stands, the probability of flying squirrel capture increased with decreasing distance to a perennial creek and increasing litter depth. The probability of flying squirrel capture also was greater with increased canopy cover in thinned stands and increased litter depth in burned stands. Greater canopy cover may provide protection from predators, thicker litter layers may harbor a greater abundance of truffles, a primary food of northern flying squirrels, and creeks may provide squirrels with food sources, drinking water and nest trees. Results from this study underscore the need for more information on the effects of forest management on northern flying squirrels near the southern extent of the species' geographic range.