The importance of natural protected areas for the preservation of locally adapted subspecies (or local genotype) of honey bees has been recently emphasized in the literature. In western Europe, initiatives have emerged to protect the native subspecies i.e., the Western European dark bee, Apis mellifera mellifera (Hymenoptera: Apidae). Here, we investigated the honey bee subspecies diversity in a Mediterranean protected area, Calanques National Park, near Marseille, France. We found that the population of honey bees is mainly composed of hybrids between Apis mellifera mellifera and Apis mellifera intermissa. These hybrids might have a better resistance to the Varroa mite and a better adaptation to arid Mediterranean climate. Before promoting the native honey bee subspecies, Apis mellifera mellifera, it appears essential to identify honey bee subspecies used by beekeepers in protected areas.