Three Ushaar genotypes from three different locations (El Maghara, Shalateen and Sant Kathrine) were screened using two different molecular Techniques; RAPD-PCR and ISSR. Both of these techniques were used to detect some molecular markers associated with the genotype identification. RAPD-PCR results, from using seven arbitrary primers, revealed 50 amplified fragments, 24 of them were polymorphic (48.00 %). The results revealed that the presence of 18 positive and 6 negative molecular markers for the genotypic
identification. ISSR-PCR results with five specific primers revealed 41 amplified fragments, 12 of them were polymorphic (29.27 %). The results
revealed that the presence of 4 positive and 8 negative molecular markers for the genotypic identification. Similarity indices and dendrogram for the genetic distances were estimated for each technique. The Similarity indices and dendrogram for the genetic distances of the combination between the two techniques revealed that the highest similarity was 44.40 % between the Ushaar
genotypes from El Maghara and Shalateen regions. Meanwhile, the lowest similarity index was between the Ushaar genotypes from El Maghara and Sant
Kathrine regions (22.20 %). The dendrogram resulting from the combination of the two techniques separated the three Ushaar genotypes into one cluster (including El Maghara and Shalateen genotypes) with the Sant Kathrine
genotype alone.