$Thymus$ $daenensis$ Celak. (Labiatae) endemic of Iran is an aromatic and medicinal plant characterized by a high concentration of thymol that is currently considered an endangered medicinal plant. The present study evaluated the intraand inter-population genetic diversity of $T.$ $daenensis$ by means of morphological and RAPD markers. The 16 primers chosen for analysis revealed 204 bands, of which 95.1% were polymorphic, indicating considerable genetic variation at the species level. In morphological study, significant difference among samples was observed. There was no correlation between clustering based on the morphological and RAPD data, while little correlation was observed between genetic divergence and geographical origins. The results of clustering based on the RAPD data showed that $T.$ $daenensis$ genotypes collected from Malayer and Arak were genetically differentiated and placed in the two separate groups. On the other hand, low intrapopulations variability and heterozygosity were detected.