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Amphibians are declining at alarming rates worldwide; however, the causes of these declines remain somewhat elusive. Here we evaluated three major threats implicated in declines of populations and disappearance of Ecuadorian amphibians: chytridiomicosis, climate change, and habitat loss. We assessed spatial patterns of these key threats to Ecuadorian amphibians using a multi-species database of endemic frogs along with information on the pathogen's distribution and environmental requirements, species sensitivity to climate change (indirectly based on species geographical distribution and ecological properties) and habitat loss. Our results show that amphibians display a non-random pattern of extinction risk, both geographically and taxonomically. Further, climate change, chytridiomicosis, and their synergetic effects, are likely currently exerting the greatest impact on amphibians in Ecuador, while habitat loss does not seem to be causing precipitous declines. The most threatened species under the IUCN extinction risk categories are exactly those that appear to be the most affected by these threats. By examining multiple potential causes of amphibian threat level in a spatially explicit framework our study provides new insights about what combination of factors are most important in amphibian declines in a tropical diversity hotspot. Further, our approach and conclusions are useful for studying declines in other regions of the world.