Thymus vulgaris L. (common thyme) is an aromatic, medicina/ and spice plant belonging to the Lamiaceae family. lts aerial parrs are considered to have bronchospasmolytic, expectorant and antibacterial effecrs and becouse of that they are common ingredient of the cough and bronchial teas and other phyropreparations. Thymus pulegioides L. (large wild thyme) has been often united with T serpyllum, but Flora Europaea clearly distinguishes these two species. The aim of this comparative study was to determine morphological, anatomical and phytochemical features required for the differentiation and identity proof of T vulgaris and T pulegioides. Based on different morphological features, the leaves in toto of T vulgaris and T pulegioides can be easily distinguished. Comparative anatomical analysi.1 showed that T vulgaris has a stem pubescerit alt round while the stem of T pulegioides is hairy on the angles only. On the lower surface of rhe thyme leaf there are characteristic warty bicellular (or tricellular) elbow-shaped covering trichomes, absent in T pulegioides. Furthermore, long multicellular covering trichomes were only found on the base of T pulegioides leaf. Thin-layer chromatography of leaf extracts revealed the presence of flavonoids, phenolic acids and monoterpenoid phenols. Characteristic features of chromatograms of flavonoids as chemotaxonomic markers enable simple and reliable identification of Thymus species studied and their preparations as well. Finally, quantitative analysis showed that the contents of total flavonoids in the leaves of T vulgaris and T pulegioides were 0,06 % and O, 1 O % respectivelly.