Whitebark pine (Pinus albicaulis) is a fundamental component of alpine and subalpine habitats in the Greater Yellowstone Ecosystem. The magnitude of current white pine blister rust (WPBR) infection caused by the pathogen Cronartium ribicola and mountain pine beetle (MPB; Dendroctonus ponderosae) impacts, combined with the effect of climate change on beetle population dynamics, are placing this foundation species in a precarious state. We collected stand- and tree-level data in three whitebark pine systems in the southern Greater Yellowstone Ecosystem to evaluate current conditions and to determine how characteristics of individual whitebark pine trees, including the presence and severity of white pine blister rust, influence host selection by the MPB. Data revealed that 45% of all whitebark pine trees sampled were dead. In addition, 67% of all trees sampled were attacked by MPB, 83% were infected with WPBR, and 62% were affected by both. Whitebark pine trees that were selected as hosts by MPB exhibited significantly greater blister rust severity than trees that were not selected. Multiple logistic regression analyses identified a complex set of tree characteristics related to host selection by MPB; in addition to rust severity, stand type (mixed species or pure whitebark pine) and tree diameter were also significant predictors of selection. The interaction among MPB selection patterns, blister rust severity, tree diameter, and stand type quantified in this study will likely continue to influence the disturbance pattern and severity in whitebark pine ecosystems in the Greater Yellowstone Area. Understanding these patterns is critical to successful management of whitebark pine forests in this region.