Northern flying squirrels (Glaucomys sabrinus) of the Black Hills National Forest (BHNF) of South Dakota represent a unique and isolated population, but little is known about the home range size and habitat use of this population. Fifty-nine northern flying squirrels (34 males and 25 females) were radio-collared and tracked during their active period, from dusk until dawn, by point sampling. Minimum convex polygons (MCPs) were determined from observation locations of squirrels with ≥15 radio-tracking locations (n  =  49). Males occupied larger home ranges (n  =  30; 11.23 ± 1.48 ha) than females (n  =  19; 6.91 ± 0.94 ha; P  =  0.02). Using the radiotelemetry data and GIS vegetation layers, habitat use (grass-shrub, aspen-birch, bur oak and pine) and structural stage class (1, 3A, 3B, 3C, 4A, 4B and 4C) selection were determined for all squirrels with ≥10 radio-tracking locations (n  =  54). Habitat selection was determined by comparing the proportion of radio-tracking locations (observed) within each habitat to the proportion of habitat within the MCPs (available) using techniques developed by Neu et al. (1974). Ponderosa pine (Pinus ponderosa), which dominates 83% of BHNF, was the only habitat used proportionally more than available. Within their home ranges northern flying squirrels also selected larger trees and more canopy cover, as well as more live trees >12.7 cm dbh, higher basal area of live trees and fewer snags. This study aids managers in understanding habitat use by northern flying squirrels in pine dominated habitat of BHNF and an isolated population at the southern edge of their range.