The survival of large and mobile species in the face of habitat loss and fragmentation depends on several factors, including the landscape configuration of subpopulations and the dispersal capabilities of the species. We performed a landscape analysis of the Bolivian Tropical Andes to determine whether remaining habitat patches were suitable in terms of ecological characteristics and potential connectivity for the long-term survival of the Andean bear (Tremarctos ornatus). First we built a ruled-based model to identify key patches or areas large enough to sustain a viable population by using knowledge of Andean bear habitat requirements and movement patterns. Second, we estimated potential functional connectivity among these areas applying a cost-distance analysis based on estimates of the resistance to movement through the landscape. Finally, we quantified the proportion of these key patches and corridor habitats within the Bolivian protected area system. The rule-based model identified 13 key patches covering 21,113 km² corresponding to a maximum estimated population of 3,165 adult bears. Using cost-distance analysis, all 13 key patches were potentially connected to ≥1 other key patch. Twelve of the patches were at least partially protected by national parks, and 40% of areas considered suitable as corridors were included within a protected area. Although the current protected area system includes suitable bear habitat, large portions of key patches and corridors are unprotected, which could eventually lead to fragmentation and habitat loss if these areas are not protected.