<p>Climate change is widely recognized as one of the main threats to biodiversity¹ and predicting its consequences is critical to conservation efforts. A wide range of studies have evaluated the effects of future climate using taxon-based metrics^3,4, but few studies to date have applied a phylogenetic approach to forecast these impacts. Here, we show that future climate change is expected to significantly modify not only species richness, but also phylogenetic diversity and phylogenetic endemism of Neotropical frogs. Our results show that by 2050, the ranges of 42.20% (<i>n</i> = 213) of species are projected to shrink and the range of 1.71% of species (<i>n</i> = 9) are projected to disappear. Furthermore, we find that areas of high SR and PD are not always congruent with areas of high PE. Our study highlights the projected impacts of climate change on Neotropical frog diversity and identifies target areas for conservation efforts that consider not just species numbers, but also distinct evolutionary histories.</p>