Characterizing genetic diversity and structure is paramount in wildlife conservation management. Surprisingly, however, there are species that, despite being intensively managed, are largely overlooked in terms of genetic makeup. The Barbary partridge (Alectoris barbara), a medium-sized galliform native to northern Africa, is one such exemplary case. Since the early 2000s, a couple of breeding farms in Morocco have been operating using wild breeders. At that time, no genetic data were available for local wild populations, nor had the founders been genetically screened. After two decades, the degree of genetic diversity of wild Barbary partridge populations remains unknown. In this study, we genotyped the mitochondrial DNA control region (ca. 1000 bp) in wild and captive A. barbara populations from Morocco. Overall, we found a high and well-distributed genetic diversity, with a moderate differentiation between captive and wild populations likely attributable to either the sharing of widespread and allegedly ancestral haplotypes or the extensive release of farm-reared individuals. Nevertheless, the occurrence of private haplotypes across all the wild populations calls for separate management. A more comprehensive sampling and the use of genome-wide loci is advisable to achieve a thorough understanding of the genetic diversity of the Barbary partridge and define management units accordingly.