Tree species are highly vulnerable to anthropogenic environmental change, and are increasingly being challenged by non-native pests and climate change. Rocky Mountain bristlecone pines are long-lived, exhibit delayed maturation, have low genetic diversity, and inhabit cold, high-elevation environments. They are threatened by the non-native disease white pine blister rust, warming temperatures, changing precipitation patterns, and altered disturbance regimes. The goal of this work was to (1) sample the range-wide genetic diversity of bristlecone pine for ex situ seed and tissue collections and research before the populations are impacted, (2) assess the health and ecological conditions of the species across its geographic range (61 stands) to provide a baseline by which to evaluate future changes, and (3) assess relationships between stand and regeneration characteristics and topographic, geographic, and climatic factors to identify vulnerabilities and proactive management interventions to increase population resilience. Local variation in topoclimate was strongly related to stand structure, composition, health, and regeneration. Bristlecone pine currently showed only minor impacts from insects and pathogens, but relationships between cone production and regeneration with climate variables suggest vulnerabilities to projected climate change. Both cone production and seedling regeneration were also linked to stand structure and ground cover that provide opportunities for proactive in situ management to increase population size to mitigate potential future climate- and pathogen-driven declines. These efforts represent the first proactive coordinated range-wide genetic collection design and forest health assessment for a threatened, but not yet impacted, tree species and offers a model for other species at risk.