We quantified the habitat characteristics associated with capture sites (2003–2006) of the state endangered northern flying squirrel (Glaucomys sabrinus) in Pennsylvania to develop management recommendations that help ensure its continued persistence in the Appalachians. In addition, we used this refined understanding of northern flying squirrel habitat to update the Pennsylvania Gap analysis model for this species. We examined habitat at both the landscape and local level and determined that northern flying squirrels preferred sites that contained mature (>95 y old) mixed coniferous forests and were adjacent to a permanent water source. In addition, sites where northern flying squirrels were captured contained significantly more overstory trees (all species), saplings and rock cover. After using these data to refine the Pennsylvania Gap model for northern flying squirrels, we reduced the primary or core habitat predicted for this species in the state by 90%. Our findings further support the reliance of this species on specialized habitat in the Appalachians and help reinforce the need to conserve and manage mature mixed-coniferous forest stands, which are threatened by exotic pests and human development throughout the region.