Amphibian chytridiomycosis has caused precipitous declines of hundreds of species worldwide1. These declines are often extremely rapid, with amphibians disappearing from sites before they are known to be infected, thus preventing the collection of real time population or infection dynamics data during the chytridiomycosis epidemic phase2. By tracking two island populations of the Caribbean endemic mountain chicken frog (Leptodactylus fallax) before, during and after the emergence of amphibian chytridiomycosis, we were able to quantify the biological impacts of a near-extinction event due to this disease, possibly for the first time. We report one of the fastest declines of any species ever recorded, with a loss of over 85% of the population in less than 18 months on Dominica and within 12 months on Montserrat. Although collected only from the last intact population ahead of the epidemic wave on Montserrat, a conservation assurance population captured a representative sample of genetic diversity from the wild population, possibly because it was genetically homogenous across this small island. The disease led to a marked loss of genetic diversity from the Dominican population. The emergence of chytridiomycosis in the mountain chicken, and its spread from one island population to the other, was predictable, but the species decline could not be prevented. This case study highlights an urgent need to mitigate the emergence and spread of wildlife disease at both national and international scales if the CBD 2020 targets for halting biodiversity loss are to be attained.