Olive (Olea europaea L.) is an economically significant fruit and oil crop in the Mediterranean region where it has been cultivated since ancient times. Two virgin olive oils were obtained from two olive cultivars i.e. “Wetagen" and “Chemlali" collecting from 15 different plants localized in Marsa Matroh and Siwa Oasis. DNA was extracted and three molecular techniques i.e. RAPD, SSR and AFLP were used to made DNA fingerprinting and calculate the genetic similarity between both oil cultivars. Data showed that, genetic similarity between the both oil cultivars was 0.13% based on the eight RAPD primers, 0.07% for AFLP primers and 0.03% for SSR markers. From these data we have been able to use these markers with oil to fingerprint and differentiate olive oils in markets. The differences found in the DNA patterns can be used as a characteristic fingerprint of each oil with the certainty that these amplifications are only obtained with olive DNA and not with DNA from any other contaminant origin.