We compared 11 ecological variables thought to be important for assessing the habitat of the endangered Virginia northern flying squirrel (Glaucomys sabrinus fuscus) at 11 occupied and 9 unoccupied sites within northern hardwood-montane conifer forests in the central Appalachians of West Virginia. Forest stands at sites occupied by G. s. fuscus had significantly higher relative importance values of montane conifers such as red spruce (Picea rubens) and little or no presence of northern red oak (Quercus rubra) than did sites that were believed unoccupied. Probabilities derived from logistic regression analyses indicated that sites were considered occupied when relative importance values of montane conifers in forest stands exceeded approximately 35%. Conversely, we detected no differences in elevation, absolute forest basal area, overstory tree species richness, total shrub density, percent coarse woody debris cover, percent herbaceous cover, percent emergent rock cover and percent soil organic matter (humus) between occupied and unoccupied sites. We observed low levels hypogeal fungi across all sites and fungi presence did not differ between occupied and unoccupied sites. Patchily distributed fungi combined with the much reduced and altered forest habitat in the region provide additional insights into the rarity of G. s. fuscus in the central Appalachians.