Recent studies have suggested that contemporary losses of species are unevenly distributed over phylogenies. Here, we show that species of Australian marsupials are at higher risk if they belong to genera that are species-poor, old or phylogenetically distinct. Extinction risk in this group is also related to habitat and body size, being higher for species from non-forested habitats and of intermediate body size. We tested the extent to which the phylogenetic selectivity of extinction was explained by this ecological pattern. We found that while genus size and distinctiveness explain no variation in extinction risk that is not accounted for by habitat and body size, there is a significant residual association of genus age with extinction risk. This suggests that while species in small and distinctive genera are at high risk because they are overrepresented in non-forested habitats and intermediate body size classes, species in old genera are at higher risk over the range of body sizes and habitats and may be intrinsically vulnerable to extinction.