Thymus is one of the most valuable medicinal and spice plants due to its application in food and pharmaceutical industries. In the present study, the diversity of 11 Thymus species was assessed by molecular, morphological and phytochemical markers. The results of analysis of variance showed significant differences among the species for morphological traits. The essential oil content of the species varied from 0.86% to 2.34% and T. vulgaris showed the highest mean of this trait. Cluster and principal component (PCA) analysis for morphological traits ) and genetic differentiation (Gst= 0.31) were observed among the species. According to the ISSR markers, T. transcaspicus exhibited the highest genetic variation (0.19), polymorphism % (57.69%), and Shannon index (0.29). Cluster and PCA analysis based on the ISSR markers classified the species in to four groups. The STRUCTURE analysis also showed high admixture of Thymus species that might be originated from high rate of natural hybridization. High polymorphism (98.3%) was observed in studied species based on the SRAP markers and cluster analysis classified Thymus species into five main groups. According to analysis of molecular variance (AMOVA), 63.14% of total genetic variation was obtained within the species, while 36.86% of variation was observed among the species. The STRUCTURE analysis was also performed to estimate the admixture of species. For instance, T. carmanicus and T. transcaspicus revealed high admixture. HPLC analysis showed the presence of rosmarinic acid (32.3-150.7 mg/100g DW) and cinnamic acid (1.7-32.3 mg/100g DW) as major phenolic acids, as well as apigenin and epicatechin as the major flavonoids in Thymus species. Cluster and PCA analysis of the components classified the species in to three groups. Finally, comparison of molecular and phytochemical markers showed similarity in some cases. For instance, T. vulgaris separated from other species according to the major polyphenolic profiles and molecular analysis. Finally, based on molecular, morphological and phytochemical information, T. vulgaris and T. carmanicus can be suggested as good candidate species for further breeding programs. Key words: Thymus, Genetic Variation, SRAP, ISSR, Morphology, Essential oil.
