We monitored 11 populations of eight species of Eleutherodactylus in Puerto Rico from 1989 through 2001. We determined relative abundance of active frogs along transects established in the Caribbean National Forest (El Yunque), Carite Forest, San Lorenzo, and in the vicinity of San Juan. Three species (Eleutherodactylus karlschmidti, E. jasperi, and E. eneidae) are presumed to be extinct and eight populations of six different species of endemic Eleutherodactylus are significantly declining at elevations above 400 m. Of the many suspected causes of amphibian declines around the world, we focused on climate change and disease. Temperature and precipitation data from 1970–2000 were analyzed to determine the general pattern of oscillations and deviations that could be correlated with amphibian declines. We examined a total of 106 tissues taken from museum specimens collected from 1961–1978 and from live frogs in 2000. We found chytrid fungi in two species collected at El Yunque as early as 1976, this is the first report of chytrid fungus in the Caribbean. Analysis of weather data indicates a significant warming trend and an association between years with extended periods of drought and the decline of amphibians in Puerto Rico. The 1970’s and 1990’s, which represent the periods of amphibian extirpations and declines, were significantly drier than average. We suggest a possible synergistic interaction between drought and the pathological effect of the chytrid fungus on amphibian populations.