Genetic relationships were evaluated among three genotypes of the Egyptian henbane (Hyoscyamus muticus L.), collected from Wadi-sudr, El Maghara and Shalateen, by employing SDS-PAGE for seed protein and peroxidase, polyphenyl oxidase and Alcohol dehydrogenase analysis. SDS-PAGE generated a total of 13 bands of which nearly 69 % were polymorphic. Identifiable polymorphic bands were detected from peroxidase, polyphenyl oxidase and Alcohol dehydrogenase analysis. However, these polymorphic markers clearly distinguished between the three genotypes from Wadi-Sudr, El Maghara and Shalateen regions. Cluster analysis using data generated by SDS-PAGE for protein, clearly separated the three genotypes collected from Wadi-sudr, El Maghara and Shalateen origin.