In this study we investigate some applications of genetic markers in animal conservation, using the Arabian oryx (Oryx leucoryx) as an example. Out of 66 sets of microsatellite primers from other ruminants, 58% were found to amplify microsatellites in Arabian oryx. Polymorphism (50% of loci amplified) and allelic diversity (mean 2.1 alleles/locus amplified) were within the range found in other ruminants. Arabian oryx (n = 343) representing most of the major groups world-wide were typed at six loci. Low but significant population differentiation was found between most oryx groups, suggesting that management of Arabian oryx has led to substantial genetic mixing between populations. Forty percent of the alleles in one additional Arabian oryx sample from the pre-extinction population in Oman were not found in any contemporary Arabian oryx, and two out of four contemporary populations were deficient in rare alleles, suggesting that the species has lost some neutral genetic variation. The microsatellite loci were sufficiently polymorphic for identification of an Arabian oryx sample in a forensic context, but were not sufficiently polymorphic for large-scale parentage inference. We suggest that it is important to evaluate whether genetic markers are likely to have sufficient power to answer particular conservation questions prior to committing conservation resources to genetic typing.