Iran itself has a well-documented history of olive (Olea europaea L.) growing dating back more than two thousand years. This country also contains a large variety of unknown olive cultivars. Morphological studies based on the method prepared by the EU RESGEN CT96/97 project, coordinated by the International Olive Oil Council (IOC) revealed that there are some homonymous in the main Iranian olive cultivars. Analysis of endocarp characteristics, which displays the most robust features, reveals a considerable degree of intra-cultivar variation within traditionally recognized Iranian cultivars. Based on the analysis carried out so far, the 10 traditional cultivars studied have been reclassified into 27 cultivars. Homonyms and mislabeling was clearly observed in 5 of 10 studied cultivars by morphological traits contain: Khormazeitoon, Rwoghani, Shengeh, Dakal and Golooleh. To evaluate the accuracy of the new morphological classification, the morphological classification examined the genetic diversity of these cultivars using 17 RAPD primers. The data analyzed using Dice similarity coefficient and the WPGMA clustering method. 4 of 17 primers (OPC 08, 15, 19, 20) produced high polymorphic bands that able to classify some new cultivars. As a conclusion, Molecular results proved the accuracy of the new morphological classification in some cultivars.