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We show, with classical morphometrical analyses, that Libyan honeybees sampled at coastal and desert locations are distinctly different from both the adjacent A. m. intermissa bee populations of Tunisia and Algeria and those of A. m. lamarckii of Egypt. The morphotype was most closely related to A. m. sahariensis and, based on wing venation angles, showed affinities to A. m. jemenitica, indicating that the sampled populations might be derived from a formerly extended Saharan honeybee population during the Holocene pluvial. Scattered morphometric similarities to the European bee A. m. ligustica suggest that importation of honeybees from Italy may have had only minor impact on endemic Libyan honeybee populations. Conservation measures might be particularly appropriate for remote oasis populations, which might be true relic population from the Holocene.