Southern flying squirrels (Glaucomys volans) use multiple nest trees for foraging and protection, but nest trees can become scarce following harvests of hardwood forests. In northern Wisconsin, the Managed Old-growth Silvicultural Study tested techniques to remediate logging impacts on forest-dependent wildlife. Three types of canopy treatments were applied (multicohort harvest [0.4-ha and 1.2-ha irregular group shelterwoods], medium gaps [18-m- and 24-m-diameter gaps], and small gaps [11-m-diameter gaps]). To evaluate the effects of treatment on nest tree selection by southern flying squirrels, we tracked 33 radiocollared southern flying squirrels once a week for 5 weeks in late summer, locating 82 nest trees (X¯ =  2.73 nest trees per southern flying squirrel [95% confidence interval: 2.28–3.18 nest trees]). Canopy treatments were important predictors of nest tree switching. Probability of switching differed by canopy treatment (listed from lowest to highest probability): multicohort harvest: 0.29 (0.17–0.42), medium gaps: 0.44 (0.32–0.56), control: 0.57 (0.41–0.73), and small gaps: 0.73 (0.61–0.85). Lower nest tree switching in the multicohort harvest compared to the small gaps likely reflected availability of habitat resources. Spatial arrangement of canopy gaps and associated effects on southern flying squirrels should be considered when planning timber harvests in northern hardwoods.