Thyme ( Thymus sp.) is a perennial herb with woody and cracked stems, cross pollinated and a member of Lamiaceae family and Nepetoidaea subfamily. Thyme essential oil is among the top ten herbal essential oils, with a special importance in the international market, and contains a range of monoterpene compounds and its isomer(s). Fourteen species of thyme have been identified in Iran that grows in different geographical and ecological regions. The highest distribution of thyme is in the north and west of Iran, while the number of species is lower in the south and east. Despite the economic and medicinal importance of this plant, limited molecular studies have been conducted to investigate the genetic variation of thyme, most of them have examined the genetic diversity of certain types of thyme in limited areas of Iran using RAPD, ISSR, ISJ and AFLP markers. So far, SCoT and SRAP markers have been used in Iran for certain thyme species, but despite their efficiency, they have not been used to study the diversity within and between thyme species. Here, we used SCoT and SRAP markers to estimate the genetic diversity among and within six Thymus species, including Th. vulgaris , Th. kotschyanus , Th. daenesis , Th. lancifolius , Th. transcaucasicus , and Th. pubescens . Eight SCoT primers and eleven SRAP primer combinations (PCs) amplified 211 and 300 fragments, respectively, of which 84.47% and 84.13% were polymorphic for all accessions. The PIC value was 0.27 and 0.374 for SCoT primers and SRAP PCs, respectively. Cluster analysis based on Jaccard’s similarity coefficient using Unweight Pair Group Method with Arithmetic mean (UPGMA), with Coffenetic coefficient of 0.81 and 0.75 for SCoT and SRAP primers, respectively, indicated a relatively wide range of diversity across the studied accessions. The results of the SCoT and SRAP markers indicated a relatively high genetic diversity and gene flow among populations (Fst= 0.11); so that the Nm calculated for SCoT and SRAP primers was 2.02. A large variety of populations indicates the presence of a source of rich germplasm for use in breeding programs. The results of population structure survey using Structure software indicated a large genetic exchange and mixing population. In conclusion, the results indicated that the Key words : Thyme, Genetic diversity, SCoT, SRAP
