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Global climate change is expected to produce large shifts in vegetation distribution and has already increased tree mortality, altering forest structure. However, long-term shifts will be partly dependent on the ability of species to reproduce under a novel climate. Few studies have examined the impact of climate change on the reproductive output of long-lived ’masting’ species, or species characterized by episodic reproductive events. Here, we show that seed cone production among pinyon pine (Pinus edulis), a masting species, declined by 40% from the 1974 decade (1969-1978) to the 2008 decade (2003-2012) in revisited stands throughout New Mexico and northwestern Oklahoma. Seed cone production was highly correlated with late summer temperatures at the time of cone initiation. Further, declines in seed cone production were greatest among populations that experienced the greatest increases in growing season temperatures, which were the populations located at the cooler, upper elevations. As growing season temperatures are predicted to increase across this region over the next century, these findings suggest seed cone production may be an increasingly important bottleneck for future pinyon pine regeneration, especially in areas with greater increases in temperature. Declines in seed cone production may not only affect pinyon pine population dynamics but also the various wildlife species that rely on pinyon pine seeds. Because pinyon pine has similar reproductive strategies as other semi-arid pine species, increasing temperature may negatively influence reproductive output of other conifers. Further investigation into the full geographic and taxonomic extent of these seed declines is warranted.