This investigation was carried out to assess the relationships among three Thymus species;two wild species (Thymus capitatusandThymus decussatus)and a cultivar(Thymus vulgaris).Two molecular markers were used to determine the genetic relationships among them; random amplified polymorphic DNA (RAPD) and the inter-simple sequence repeats (ISSR) markers techniques. The results suggest that RAPD marker is the best choice for the evaluation of diversity and the genetic relationships between two wild Thymus specieswith high accuracy, which revealed 224 DNA bands detected across 15primers with high polymorphism than ISSR, which revealed 336DNA bands. The genetic relationship among Thymus speciesbased on molecular data was developed using a dendrogram constructed by UPGMA cluster analysis.   Conservationist may use the information of the present study to make effective decisions regarding the global protection and management of Thymus speciesin Egypt.