Madagascar is a top global conservation priority for high rates of deforestation and endemism. Deforestation has been extensive, but impacts of forest loss on biodiversity have not been well quantified, especially for nonvertebrates. We use generalized dissimilarity modeling (GDM) as a basis for estimating forest biodiversity remaining at different points in time. We predict that 9.1% of species in Madagascar have been committed to extinction from deforestation between 1950 and 2000. This quantity is higher than losses expected from random deforestation of the same total area, indicating that deforestation has been biased towards environmentally and biologically distinct areas. In contrast to traditional area-based methods, these techniques allow one to estimate biodiversity loss based on the location of deforestation and thus can inform land-use policies that aim to minimize biodiversity impacts of deforestation or development.