Habitat destruction and degradation are major factors in reducing abundance, placing populations and species in jeopardy. Monitoring changes to habitat and identifying locations of habitat for a species, after disturbance, can assist mitigation of the effects of human-caused or -amplified habitat disturbance. Like many areas in the western United States, the Pinaleño Mountains of southeastern Arizona, USA, have suffered catastrophic fire and large-scale insect outbreaks in the last decade. The federally endangered Mt. Graham red squirrel (Tamiasciurus hudsonicus grahamensis) is only found in the Pinaleño Mountains, and to assess effects of forest disturbance on habitat we modeled their potential habitat by identifying characteristics of cover surrounding their centrally defended middens. We classified high-spatial resolution satellite imagery into ground cover classes, and we used logistic regression to determine areas used by squirrels. We also used known midden locations in conjunction with slope, elevation, and aspect to create a predictive habitat map. Squirrels selected areas of denser forest with higher seedfall for midden sites. Among active middens, those in the densest and least damaged forests were occupied in more seasons than those in more fragmented and damaged areas. The future conservation of red squirrels and the return of healthy mature forests to the Pinaleño Mountains will rely on preservation of mixed conifer zones of the mountain and active restoration of spruce–fir forests to return them to squirrel habitat. Our ability to evaluate the spectrum of fine- to coarse-scale disturbance effects (individual tree mortality to area wide boundaries of a disturbance) with high-resolution satellite imagery shows the utility of this technique for monitoring future disturbances to habitat of imperiled species.