In this study, we examined phenotypic and genetic relationships between 15 Thymus species including T. canoviridis, T. haussknechtii, T. fallax T. leucotrichus, T. pubescens, T. pseudopulegioides, T. sipyleus, T. convolutus, T. spathulifolius, T. cappadocicus, T. brachychilus,, T. kotschyanus, T. fedtschenkoi, T. migricus, T. transcaucasicus wildly growing in Eastern Anatolia region of Turkey by using Fatty acid (FAMEs) and RAPD profiles. According to the gas chromatography results, 16:0, 19:1:omega 9t fatty acids were found in almost all analyzed thymus species. Also, C9 Dicarboxylic acid was observed in all species except for T. transcaucasicus, T. pubescens T. haussknechtii, T. convolutus, T. fallax. Moreover some fatty acids like 15:0 iso, C20 N alcohol, and C25 N alcohol were only observed in T. leucotrichus, T. haussknechtii, T haussknechtii respectively (38, 28; 37, 40; 14, 78). On the other hand, RAPD analysis was carried out in 15 Thymus species. Twenty oligonucleotide primers were screened on Thymus, and among them, 7 primers showed clear polymorphic patterns. Cluster analysis of Thymus species was performed based on data from polymorphic RAPD hands, by using Jaccard's similarity coefficient. A similarity matrix showed that the highest genetic similarity (0.077) was between T. canoviridis and T. haussknechtii and the least (0.867) was between T. convolutus and T. transcaucasicus. In addition to this, three genetically distinct groups were determined between Thymus species.