Balanites aegyptiaca (L.) Delile or desert date (Zygophyllaceae) is widely distributed in arid and semi-arid regions in Africa and South Asia. It is native to all drylands south of the Sahara desert. It is a prickly tree that plays an important role in conserving and renewing damaged vegetation cover. According to previous studies, B. aegyptiaca were identified for five varieties based on the leaflet colour, the pubescent, the spine length, the number of flowers per inflorescence, and the fruit size and shape. Recently, the varieties were reduced into two, depending on the characters mentioned above and the insertion of inflorescence. The current study aimed to verify the infra-specific variation between B. aegyptiaca samples collected from Egypt and Saudi Arabia. A complementary approach using a detailed macro- and micromorphological analysis of leaflets, petioles, stems, spines, and fruits was performed for comparative studies in plant collections using a light microscope and scanning electron microscope (SEM). Statistical analysis was carried by using R- software. The preliminary results showed a remarkable variation in the leaflet area and shape, the number of the leaflet vascular bundles, the presence/ absence of cavities in the petiole cross-section, the stomatal characters, and the type and density of both trichomes and the epicuticular waxes.