Climate change: The effects of current and future climatic conditions on Great Basin Bristlecone Pine regeneration are uncertain. Climate change may be hindering regeneration on sites in the interior Great Basin.

The best development of Great Basin Bristlecone Pine forests occurred during the Pleistocene, when the climate was both cooler and wetter. Extensive forests extended down mountain slopes in the Great Basin, and Great Basin Bristlecone Pines occupied Mojave Basin mountain slopes, where they are now absent.

Mountain top stands, lower elevation stands, or stands now on marginal sites may be threatened by climate change, though it is difficult to predict the complex interactions of changes in temperature, precipitation patterns, and shifting insect and disease ranges. In many places, potential habitat occurs upslope of existing populations, indicating potential for upslope shifts in distribution to accommodate a warming climate. Lower elevation populations could potentially be compromised by black stain, introduced by upslope movement of pinyon pine. Shifting patterns of various insects and diseases in response to long term changes in temperature and/or precipitation could affect existing stands, particularly at the current lower tree limit.

Blister rust: Bristlecone Pine is one of the five-needle pines susceptible to the exotic pathogen, White Pine Blister Rust (Cronartium ribicola A. Dietr.). Blister rust resistance is being evaluated at the USDA Forest Service, Institute of Forest Genetics, Placerville, CA. Preliminary results show no evidence of the hypersensitive response with 30% of the seedlings canker-free. Both Rocky Mountain Bristlecone Pine (Pinus aristata Engelm.) and Great Basin Bristlecone Pine are highly resistant to blister rust, in part due to wax-occluded stomata. In addition, the predominant alternate host, Ribes cereum, is highly resistant to infection by aeciospores, thereby making it difficult for the rust to complete its life cycle in the alternate host. However, levels of resistance of Great Basin Bristlecone Pine to blister rust remain unclear. Laboratory studies have shown Great Basin Bristlecone Pine seedlings to be lacking key alleles that confer genetic resistance to blister rust. Populations in the White and Inyo Mountains, which lie close to moderately high infection centres in the Sierra Nevada, may be at greatest risk for blister rust infection and spread.

Other insects and/or disease agents: Mountain pine beetle, dwarf mistletoe, wood-rot basidiomycetes and wood decay fungi are all known to infest Great Basin Bristlecone Pine. The dry high-elevation sites of most Great Basin Bristlecone Pine currently serve to slow fungal growth and wood decay.

Wildland fire: based on its thin bark, Great Basin Bristlecone Pine is adapted to survive only low-severity surface fires. With low productivity and widely spaced stands, there are usually not enough fuels to carry fire in high-elevation Great Basin Bristlecone Pine sites. When fires do occur at high elevations, they are typically small, low-severity surface fires. Stand dynamics in these areas are generally more influenced by climate and seed dispersal patterns than by fire.

In contrast, fuels are sufficient to carry fire in denser, lower-elevation sites where Bristlecone Pine occurs in mixed forests. Little documentation exists of post-fire establishment, growth rate, and successional role of this species. Post-fire establishment may be favoured on mixed conifer ecotones, lower-elevation limestone soils, and other sites that are marginally productive for other conifer species but relatively good for Great Basin Bristlecone Pine. Further research is needed on this topic.

Commercial timber production: Though Great Basin Bristlecone Pine-limber pine forests were logged in the 1860s for structural timber, the species is no longer commercially important as a timber product.