A quarter of all lagomorphs (pikas, rabbits, hares and jackrabbits) are threatened with extinction, including several genera that contain only one species. The number of species in a genus correlates with extinction risk in lagomorphs, but not in other mammal groups, and this is concerning because the non-random extinction of small clades disproportionately threatens genetic diversity and phylogenetic history. Here, we use phylogenetic analyses to explore the properties of the lagomorph phylogeny and test if variation in evolution, biogeography and ecology between taxa explains current patterns of diversity and extinction risk. Threat status was not related to body size (and, by inference, its biological correlates), and there was no phylogenetic signal in extinction risk. We show that the lagomorph phylogeny has a similar clade-size distribution to other mammals, and found that genus size was unrelated to present climate, topography, or geographic range size. Extinction risk was greater in areas of higher human population density and negatively correlated with anthropogenically modified habitat. Consistent with this, habitat generalists were less likely to be threatened. Our models did not predict threat status accurately for taxa that experience region-specific threats. We suggest that pressure from human populations is so severe and widespread that it overrides ecological, biological, and geographic variation in extant lagomorphs.