The genetic diversity of two populations of Moringa peregrina in South Sinai was performed by inter-simple sequence repeat markers (ISSR) using ten primers. The investigation was carried out as a primary step towards developing effective conservation strategies for the protection of Moringa peregrina germplasm. The aim of this study was to assess the genetic diversity within and among twenty individuals of Moringa peregrina collected from two populations in Wadi Zaghra and Wadi Feiran, South Sinai. The ISSR marker analysis showed a significant level of genetic variation within and among the populations, reached 95.45% of polymorphism. Cluster analysis was performed to construct a dendrogram using UPGMA. The dendrogram clustered the individuals into two major clusters, the first one for Wadi Zaghra individuals (about 78% polymorphism) and the second one for Wadi Feiran individuals (about 75% polymorphism). The obtained results indicate the high genetic diversity between the individuals of Moringa peregrina in South Sinai.