Amphibian populations have been declining worldwide and the exact mechanisms underlying these changes are not well understood. We examined environmentally induced phenotypic changes that may reflect ongoing stresses on individuals and therefore their ability to persist in increasingly changing landscapes. Specifically, we evaluated the contribution of habitat loss on the size, allometry, and levels of fluctuating asymmetry of Eleutherodactylus antillensis and E. coqui, 2 common species that are endemic to Puerto Rico. We x-rayed frogs collected at 9 sites that differed in the amount of forest cover and measured their snout-vent, radio-ulna, femur, and tibio-fibula lengths. E. antillensis and E. coqui were smaller in the highly disturbed (< or =20% forest cover) than in the intermediately (20-70% forest cover) and little-disturbed (> or =70% forest cover) landscapes. In E. antillensis but not in E. coqui, the slope and intercept of the curves relating snout-vent length with the length of the 3 bones differed with degree of forest cover, suggesting an effect of habitat loss on body shape. In E. antillensis and E. coqui, differences between right and left sides corresponded to true fluctuating asymmetry; however, only the radio-ulna length of E. coqui showed a trend toward an increase in fluctuating asymmetry with habitat loss. Because body size scales with a variety of physiological, life history, and ecological traits, conservation programs aimed at monitoring morphological changes in amphibians may help in understanding the mechanisms that contribute to their persistence in changing environments.