AbstractThe aoudad (Ammotragus lervia) is a Vulnerable bovid endemic of North Africa. Although legally protected in almost every country of its native distribution, the aoudad continues to be hunted for meat and trophy in both North Africa and the countries where it has been introduced. The species was subject to past translocations planned irrespectively of the genetic diversity and local adaptations of source and receiving populations, and no management or conservation units have ever been designed. We aim to provide here important insights on the taxonomy of the aoudad subspecies and the genetic diversity of most of its wild and captive populations. We collected 127 invasive and non-invasive samples from five of the six subspecies of aoudad recognized to date. We could successfully retrieve genetic data for 74 samples. Of those, 36 provided both nuclear (11 microsatellites) and mitochondrial (Cyt-b) data, 31 just nuclear data, and six just mitochondrial data. We implement Bayesian approaches to infer the population structure and phylogenetic relationships between the different populations/subspecies and backtrack the maternal lineages of introduced individuals in European populations. Our results support the presence of four genetically different wild populations, corresponding to three distinct mitochondrial lineages plus a fourth group restricted to Egypt identified by the nuclear markers. We also provide genetic evidence on the affiliation of some introduced European populations with respect to the native ones. The genetic diversity instead of variation within all wild populations was low. This might be a consequence of small effective population size and/or high inbreeding degree, probably related to hunting, decline in habitat availability and quality (i.e. overgrazing, and frequent drought), and high inbreeding degree. Our results provide important information for the aoudad conservation, including reintroductions and reinforcement actions of wild populations, and the exchange of individuals among captive stocks.