Glaucomys sabrinus coloratus (Carolina Northern Flying Squirrel) is a federally endangered subspecies that occurs in high elevation forests of the southern Appalachian Mountains. Denning sites may be a limiting factor for this subspecies in areas where cavity trees are not abundant or where interspecific competition from other tree squirrels occurs. This shortage can result in use of unusual denning sites, such as subterranean dens. Herein, we report atypical denning habits of radio-collared Carolina Northern Flying Squirrels in southwestern Virginia and western North Carolina from 2008 to 2011 and 2014. Increased knowledge of denning habitats may be beneficial for conservation and habitat management of this subspecies, particularly in sub-optimal or degraded habitats.