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Abstract Aim To understand how the biophysical environment influences patterns of infection by non-native blister rust (caused by Cronartium ribicola) and mortality caused by native mountain pine beetles (Dendroctonus ponderosae) in whitebark pine (Pinus albicaulis) communities, to determine how these disturbances interact, and to gain insight into how climate change may influence these patterns in the future. Location High-elevation forests in south-west Montana, central Idaho, eastern and western Oregon, USA. Methods Stand inventory and dendroecological methods were used to assess stand structure and composition and to reconstruct forest history at sixty 0.1-ha plots. Patterns of blister rust infection and mountain pine beetle-caused mortality in whitebark pine trees were examined using nonparametric Kruskal–Wallis ANOVA, Mann–Whitney U-tests, and Kolmogorov–Smirnov two-sample tests. Stepwise regression was used to build models of blister rust infection and mountain pine beetle-related mortality rates based on a suite of biophysical site variables. Results Occurrence of blister rust infections was significantly different among the mountain ranges, with a general gradient of decreasing blister rust occurrence from east to west. Evidence of mountain pine beetle-caused mortality was identified on 83% of all dead whitebark pine trees and was relatively homogenous across the study area. Blister rust infected trees of all ages and sizes uniformly, while mountain pine beetles infested older, larger trees at all sites. Stepwise regressions explained 64% and 58% of the variance in blister rust infection and beetle-caused mortality, respectively, indicating that these processes are strongly influenced by the biophysical environment. More open stand structures produced by beetle outbreaks may increase the exposure of surviving whitebark pine trees to blister rust infection. Main conclusions Variability in the patterns of blister rust infection and mountain pine beetle-caused mortality elucidated the fundamental dynamics of these disturbance agents and suggests that the effects of climate change will be complex in whitebark pine communities and vary across the species’ range. Interactions between blister rust and beetle outbreaks may accelerate declines or facilitate the rise of rust resistance in whitebark pine depending on forest conditions at the time of the outbreak.