The looming mass extinction of biodiversity in the humid tropics is a major concern for the future, yet most reports of extinctions in these regions are anecdotal or conjectural, with a scarcity of robust, broad-based empirical data. Here we report on local extinctions among a wide range of terrestrial and freshwater taxa from Singapore (540km2) in relation to habitat loss exceeding 95% over 183 years. Substantial rates of documented and inferred extinctions were found, especially for forest specialists, with the greatest proportion of extinct taxa (34-87%) in butterflies, fish, birds and mammals. Observed extinctions were generally fewer, but inferred losses often higher, in vascular plants, phasmids, decapods, amphibians and reptiles (5-80%). Forest reserves comprising only 0.25% of Singapore's area now harbour over 50% of the residual native biodiversity. Extrapolations of the observed and inferred local extinction data, using a calibrated species-area model, imply that the current unprecedented rate of habitat destruction in Southeast Asia will result in the loss of 13-42% of regional populations over the next century, at least half of which will represent global species extinctions.