Thymus daenensis i a medicinal, aromatic plant endemic to Iran. Fourteen species of Thymus have been recognized in Iran distributed in different geographical and ecological regions of the country. Among these species T.daenensis is widely distributed in western Iran and has extensive pharmaceuticals application. Information on the levels of genetic variation within and among natural populations provides fundamental insights on the establishment of effective and efficient conservation strategies. Molecular markers are extensively used for basic and applied studies such as fingerprinting, allelic integration, selection of useful traits and genetic variation of medicinal plants. RAPD primers can quickly generate a large number of score able loci per single assay and generally give significant coverage of the genome without DNA sequence information. In this study, ninety accessions from 19 populations of T.daenensis collected from different geographical regions of Iran were studied. Sixteen primers were used to amplify 145 bands out of which 127 (87%) were polymorphic. The selected primers generated 127 amplified fragments, with an average of 9.06 fragments per primer in the whole genotypes. The size range of the amplified products was 200-1250 bp, and the number of products per primer varied from 4 for OPA-01 to 16 for CGS-33. The average PIC value for the amplification products was 0.424.nei´s gene diversity and shanon´s information Index were calculated and their values were 1.53 and 0.449, respectively. The analysis of molecular variance (AMOVA) among populations, based on specific geographical regions, showed that majority of the genetic variance found was within populations. Data obtained were used to estimate genetic similarity using the jaccard coefficient, and dendrogeram was constructed using the UPMGA method. Populations from Isfahan and Charmahal provinces had the highest and the lowest genetic diversity respectively. Cluster and PCOA analyses showed that most genotypes were groupedbased on their geographical divergence. Key words: Thymus daenensis , Medicinal plant, RAPD marker, Genetic diversity
