SUBSTANTIAL variation, in morphological traits was observed among 20 populations of A. fragrantissima in Egypt. Such variation was reflected in the clustering of the examined populations as major groups, one representing populations in the mountainous area of South Sinai and the other populations growing at lower elevations in the middle of Sinai and the desert west of the Suez canal from Suez in the east to Cairo in the west. Five populations in the eastern part of Sinai near Nuwieba and Taba on the Gulf of Aqaba were loosely assigned to the first group. The clustering of A. fragrantissima populations based on ISSR markers also showed two major groups more or less similar to the groups obtained from the analysis of morphological traits. The populations growing at high elevations in South Sinai, under lower temperature and higher humidity, were characterized by high number of total and polymorphic ISSR markers compared to other populations. Unique ISSR markers were observed in the fingerprinting of seven populations including five populations growing in the high mountains of Saint Catherine area in South Sinai and two populations growing at low elevation South east of Cairo. A noteworthy observation is that unique bands are found in populations that possess traits associated with plant size and seed yield as well as better vigor. These are important criteria for selection of populations for conservation and commercial use of A. fragrantissima.