Thymus daenensis Celak. (Lamiaceae) is an aromatic medicinal plant endemic to Iran, intensively utilized because of its wide ranging medicinal and culinary properties. The aerial parts of wild populations of T. daenensis were collected from different populations in Isfahan and Chaharmahal and Bakhtiari provinces, Southwest and Central Iran. The thymol and carvacrol amounts ranged between 13.89 to 35.89 mg g-1 and 6.88 to 23.54 mg g-1 respectively, for populations collected from various elevations. Also, our investigation showed that plant height and date of flowering between populations of T. daenensis had significant difference. The cluster analysis showed that the amount of thymol and carvacrol, and plant height of T. daenensis could be grouped into two distinctive clusters. The results indicate that the amount of thymol and carvacrol of T. daenensis are strongly affected by environmental conditions. Since secondary metabolites are the product of a predominantly biological process further studies are needed to evaluate if the reported characteristics of each population are maintained at the level of individual plants and along the breeding and selection program when grown under different soil and climatic conditions.