Differential responses by species to modern perturbations in forest ecosystems may have undesirable impacts on plant-animal interactions. If such disruptions cause declines in a plant species without corresponding declines in a primary seed predator, the effects on the plant could be exacerbated. We examined one such interaction between Pinus albicaulis (whitebark pine), a bird-dispersed, subalpine forest species experiencing severe population declines in the northern part of its range, and Tamiasciurus hudsonicus (red squirrel), an efficient conifer seed predator, at 20 sites in two distinct ecosystems. Hypotheses about squirrel habitat preferences were tested to determine how changes in forest conditions influence habitat use and subsequent levels of predispersal cone predation. We performed habitat selection modeling and variable ranking based on Akaike's information criterion; compared the level and variance of habitat use between two forest types (P. albicaulis dominant and mixed conifer); and modeled the relationship between P. albicaulis relative abundance and predispersal cone predation.