The use of restocking of animals is common practice in the management of populations subject to hunting or recreational fishing. This practice encompasses the release of large numbers of individuals in an area where the species already exists, and thus it can have detrimental genetic impacts on the target populations, especially when captive-reared animals are involved. To better understand this practice and its conservation implications, we chose as a model the wild rabbit (Oryctolagus cuniculus), a species of high economic and ecological importance, and often under intense management for hunting or conservation purposes, particularly after the large decline caused by rabbit hemorrhagic disease in the 90′s. We studied the genetics of rabbit populations in an area where restocking with captive, wild–domestic hybrids was common. We collected a total of 503 samples from 15 hunting estates that had experienced differing restocking levels, as well as from five locations with no historical restocking and five game farms. All samples were analyzed to determine the mitochondrial DNA (mtDNA) lineage typical of the two European wild rabbit subspecies and domestic rabbit. Game farms and never restocked populations were very different in their haplotypic composition. In restocked areas, the proportion of the domestic lineage was higher when releases were recent and repeated, but this declined rapidly over time, in part due to selective removal by hunting. The extended use of this practice, considering the pronounced genetic and genotypic differences between domestic and wild rabbits, represents a potential danger to natural populations, especially given the marked decrease in wild rabbit numbers experienced in recent years in its original distribution range.