In Morocco, there are two well-recognised honey bee (Apis mellifera L.) subspecies: A. m. intermissa in the north and A. m. sahariensis in the south-east. The latter subspecies is found in the arid and semiarid climates of the Sahara Desert. In this study, we used honey bees from four areas of south-eastern Morocco which are, to some degree, isolated by arid zones. We analysed the shape and size of the forewings, using the method of geometric morphometrics. The bees from the four areas of south-eastern Morocco differed significantly in terms of wing shape. Moreover, bees from traditional hives were smaller than those from modern hives. The bees from south-eastern Morocco were clearly different from the reference samples obtained from the Morphometric Bee Data Bank in Oberursel, Germany, representing most of the global variation in honey bees. Surprisingly, the bees were also different from A. m. sahariensis, which should occur in the study area, according to earlier studies. This difference could have been caused by introgression with non-native subspecies imported by beekeepers. The distinct honey bees from south-eastern Morocco deserve to be protected. We provide a method for identifying them, which can help protect them.