The present work was conducted to study the differences in leaves oil content as well as its fatty acids composition. Also, study the molecular genetic identification of three Egyptian olive Cultivars (Olea europaea L.) coined as Maraki, Aggezi Shami and Toffahi cultivated in the farm of Horticulture Research Institute. The oil content percentages in the dry leaves were (7.650, 6.046 and 4.754) for Maraki, Aggezi Shami and Toffahi, respectively. The main component of fatty acids were Linolenic acid methyl ester, Oleic acid, and palmitic acid. For molecular studies RAPD and ISSR-PCR were performed and efficient in detecting polymorphism and genetic variations within and between olive cultivars. In RAPD analysis, 4 selected primers displayed a total of 51 amplified fragments, in which 31 (60 %) were polymorphic fragments. Twenty eight out of 51 RAPD-PCR fragments were found to be useful as cultivar specific markers. Regarding the ISSR analysis, total of 46 out of 84 ISSR fragments were polymorphic. Twenty nine DNA amplified fragments were considered as cultivar-unique markers. Genetic similarities among the olive cultivars were estimated according to the fragments. In conclusion, both RAPD and ISSR polymorphisms could be used as efficient tools for the detection of similarities and phylogenetic relationships of the studied genotypes, which could be useful in the future breeding programs.