Estimates of species extinction due to human impact on tropical forests have previously been based on the relationship between species number and area. Here we use a different approach to estimate loss of tree species in the Atlantic forest of northeast Brazil. We evaluate the characteristics of plant species, their avian dispersers and the distribution of the forest remnants on the landscape to estimate that about 33.9% of tree species in this region will become extinct on a regional scale. Because northeast Brazil is the most threatened sector of South American Atlantic forest, our results highlight the need to change the current conservation paradigm for this region. Rather than focus on the creation of isolated reserves in any medium-to-large forest remnant, a bioregional planning approach is urgently required to rescue this unique biota from extinction.