The rising sea level at the end of the Pleistocene that created the islands of the Sunda Shelf in Indonesia and Malaysia provides a natural experiment in community disassembly and offers insights into the effects of body size and niches on abundance, distribution, and diversity. Since isolation, terrestrial mammal communities of these islands have been reduced by extinction, with virtually no offsetting colonization. We document three empirical patterns of disassembly, all of which are significantly different from null models of random assembly: (i) a diversity-area relationship: the number of taxa is strongly and positively correlated with island area; (ii) nested subset composition: species that occur on small islands tend to be subsets of more diverse communities inhabiting larger islands; and (iii) body size distributions: species of intermediate body sizes occur on the greatest number of islands, and smaller islands have smaller ranges of body sizes, caused by the absence of species of both very large and extremely small size. These patterns reveal the role of body size and other niche characteristics, such as habitat requirements and trophic status, in the differential susceptibility of taxa to extinction.