Zoos and related institutions make important contributions to the conservation of global biodiversity. However, resource constraints have led to certain faunal groupings being better represented in ex situ breeding programmes than others. Some broad patterns of faunal representation in zoos have been identified, although finer-scale differences within taxonomical families remain poorly understood, as do the influence of many geographical and ecological factors. Using a novel paired-species comparison approach, we investigate for the first time how seven of these variables can influence the current representation of mammal and bird species in zoos. Using data from 550 high-quality zoos worldwide, we identified 165 mammal and 228 bird species held in zoos that could be paired with clearly identifiable closest relatives not currently held in zoos. These matched pairs were then compared for threat level, zoogeographical distribution (including global hotspot endemism), spatial range, body mass, island habitat and altitudinal range. Results indicate that mammal and bird species in zoos are, on average, not only larger than their close relatives not held in zoos, but also possess larger spatial ranges, are less likely to be endemic and are distributed in lower-risk geographical regions. Importantly, they also tend to be less, rather than more, threatened with extinction. Multivariate models confirm that many of these correlated predictors act independently. We suggest that key mechanisms which can increase the inherent conservation risk of mammal and bird species can also act as barriers to their representation in zoos, and that this may contribute to a disparity between where ex situ resources are spent and where they are most needed.