The precipitous decline of the keystone species whitebark pine (Pinus albicaulis Engelm.) has resulted in dramatic changes to many high elevation ecosystems in the western U.S. and Canada. To restore these ecosystems, there is a need to establish populations of whitebark pine that will persist in the face of both natural and anthropogenic disturbances (e.g. climate change, white pine blister rust [Cronartium ribicola J.C. Fisher]). The listing of whitebark pine as endangered in Canada and its recent proposed listing as threatened in the U.S. reinforce the urgency of the need to act. This paper presents a six-step methodology for whitebark pine restoration planning in a GIS environment, that was developed as a pilot on a 5-million-acre (2-million-hectare) subset of the Crown of the Continent Ecosystem (CCE). The methodology synthesizes the best available datasets and science into a flexible, data-informed decision-making process that can be applied consistently across large geographic areas. The end-product is an action plan that guides implementation of treatments with a high likelihood of success at an appropriate scale to address the enormous need for restoration. The methodology begins by mapping where whitebark is capable of existing, then quantifies the priority conservation values it provides, the stressors affecting those conservation values, and how those stressors could affect the likelihood of restoration treatment success. Based on those results, priority core areas for restoration are identified. Finally, a restoration plan assigns and prioritizes site-specific actions that protect and restore genetically diverse, evolutionarily stable populations of whitebark pine that are well-distributed across the area of interest. This methodology can be scaled up as demonstrated by its use to identify core areas in Region 1 of the USDA Forest Service. It can also be applied to other species as demonstrated by the addition of limber pine (Pinus flexilis James) when the methodology was used to develop a restoration strategy for the full 18-million-acre (7-million-hectare) CCE (Summary Report in progress).