Chemical composition of essential oils from five populations of Thymus daenensis Celak. subsp. daenensis, an important medicinal plant endemic to Iran, was investigated by means of GC and GC/MS. All oils were characterized by a high content of monoterpenoid compounds, especially oxygenated ones (75.4–83.0%), and a small amount of sesquiterpenes (1.7–4.0%). Thymol was identified as the major component of all essential oils. Cluster analysis based on the percentage composition of essential oils and data obtained from the RAPD molecular markers experiment led to clearly discrimination of Th. deanensis populations and they were placed into two main clusters; members of the first cluster (Arak and Malayer) contained thymol as the main oil component (77.7–78.1%), whereas the populations included in the second cluster (Aleshtar, Hamedan and Dena) were rich in carvacrol (19.1–29.4%) as well.
