Moringa peregrina is an economically valuable tree of Egyptian deserts. It is used medicinally, provides a highly nutritious supplement to Bedouin diets, provides fodder for livestock, and is used for fire wood. M. peregrina seeds have been a source of high-quality oil for cosmetics and perfumes since antiquity. Due to unmanaged grazing and over-collection, M. peregrina has become one of the most endangered tree species in the Egyptian desert ecosystem. A long-term conservation program is urgently needed to maintain or increase the number and size of M. peregrina populations. Ten populations harboring a total of 130 adult M. peregrina were sampled from three disjunct Wadis in South Sinai (W. Me'ar, W. Fieran and W. Zaghra). Open-pollinated seedlings were electrophoretically analyzed to address two basic questions: (1) how is genetic diversity distributed within and among populations within these three Wadis; and (2) what is the mating system of this species. M. peregrina has a mixed mating system with a selfing rate up to 16% and has limited genetic diversity within and significant genetic differentiation among its populations, the majority of which occurs among Wadis. Direct protection is urgently needed to decrease genetic deterioration within M. peregrina populations and to improve their ability to maintain or improve their population numbers. The priority of in situ conservation should be to conserve a few large well-distributed populations representing different Wadis. Ex situ germplasm collections should be made across the species' range to ensure a representative sample of its genetic variation. Seed orchards designed to maximize cross-fertilization among unrelated individuals should be established to generate propagules to supplement natural populations.