Only approximately 2600 black rhinoceros survive today, mainly in small, isolated populations of < 100 animals. The management of remaining black rhinoceros populations aims at preserving natural levels of genetic relatedness and optimizing breeding success, which requires an accurate knowledge of the mating system, reproductive skew and effective population size. DNA was extracted from faecal samples from a community of 35 wild black rhinoceros, and microsatellites were used to characterize patterns of paternity of 19 offspring born from eight females in this community. Paternity could be ascribed unequivocally for each offspring. Although our conclusions must be considered tentative, we present the first genetic evidence that black rhinoceros males are polygynous, with a high variance in reproductive success. We also describe a noninvasive management tool that can be used for the genetic management of this critically endangered species, both in the wild and in captivity.