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 nesting ecology of this population. We radio-collared 59 northern flying squirrels and collected a daytime nest location every 2–4 wk during May through Aug., 2005 through 2007. The radio-collared northern flying squirrels used 133 different nests, including drays in live trees, cavities in live trees and cavities in snags. We examined distance between consecutively located nests and characteristics of nest trees to random and available trees within the northern flying squirrels' home ranges. The distance between consecutively located nests was farther for males than females. Sixty-eight percent of the nests used were in cavities. Snags and larger trees were selected for nest sites more than expected based on availability. This study will help managers understand an aspect of microhabitat resource use by northern flying squirrels in ponderosa pine (Pinus ponderosa) dominated habitat of BHNF and an isolated population at the southern edge of their range.