Three Egyptian henbane genotypes from three different locations (Wadi Sudr, El Maghara and Shalateen) were screened using two different molecular Techniques; RAPD and ISSR. Both of these techniques were used to detect some molecular markers associated with the genotype identification. RAPD results, from using seven arbitrary primers, revealed 57 amplified fragments, 30 of them were polymorphic (52.63 %). The results revealed the presence of 21 positive and 9 negative molecular markers for the genotypic identification. ISSR results with five specific primers revealed 41 amplified fragments, 15 of them were polymorphic (36.59 %). The results revealed the presence of 13 positive and 2 negative molecular markers for the genotypic identification. The Similarity indices and dendrogram for the genetic distances of the combination between the two techniques revealed that the highest similarity was 68.90 % between the henbane genotypes from El Maghara and Shalateen regions. Meanwhile, the lowest similarity index was between the henbane genotypes from El Maghara and Wadi Sudr regions (8.90 %). The dendrogram resulting from the combination of the two techniques separated the three henbane genotypes into one cluster (including El Maghara and Shalateen genotypes) with the Wadi Sudr genotype alone.
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