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The bat family Mormoopidae includes three species with distributions in the Caribbean. These taxa—Mormoops blainvillei, Pteronotus parnellii, and P. quadridens—roost predominantly in hot cave chambers where temperatures may reach 40° C and humidity is close to 100%. We tested the hypothesis that mormoopid bat extirpations in this region were due to climatic changes and the loss of suitable cave environments due to flooding caused by sea level rise associated with the late Pleistocene to Holocene (ca. 10 ka) climate change transition. Ecological niche models (ENMs) were developed to estimate the current, mid-Holocene, and Last Glacial Maximum distributions of these three bat species and to assess whether suitable climatic habitat for these taxa had been stable across time in the Caribbean. Additionally, we examined the importance of karst formations (where hot caves typically form) as a predictor for the distributions of Caribbean mormoopid bats. Our results show that mormoopid bat distributions in the Caribbean have remained relatively stable over time with climate ENMs indicating up to a 19% expansion in the amount of suitable habitat from late Pleistocene to the present. Presence of karst was a good predictor when used alone or when combined as karst-climate ENMs. Fossil evidence shows that some populations of mormoopids became extirpated as recently as 3.6 ka. These data, taken together with our conclusion that suitable climate habitat for mormoopid bats existed in the Caribbean beyond late Pleistocene to Holocene transition, suggest that these bats may have survived this climate change event by roosting outside their characteristic hot cave environment.