The present investigation aimed to use RAPD and ISSR techniques that depend on the polymerase chain reaction technique (PCR) to analyze the genetic variation between Naomi and Sensation mango cultivars. RAPD revealed a total number of 105 DNA band, fifteen bands of them were polymorphic and the average number of the polymorphic bands were seven bands / primer. ISSR primers clarify a wide range of variance between the studied cultivars, ISSR was able to recognize 124 DNA bands and thirty-two out of them were polymorphic with polymorphism percentage 25.8% and average polymorphic bands 10.3 / primer. Also, RAPD detected a high genetic similarity between Naomi and Sensation (91.4); while, ISSR detected 82.4%. RAPD and ISSR identify unique DNA bands distinguish between the two studied cultivars and could be used as a fingerprint for both cultivars. Naomi and Sensation cultivars were distinguished by 15 positive unique markers. The Naomi cultivar was identified by 14 positive markers and 4 negative markers. On the other hand Sensation was able to detect 14 negative unique markers and 4 positive one. The four negative unique markers resulted from three primers (OPO09, OPG06, OPG09), the size of these markers ranged from 200bp -280 bp.