The study was conducted to optimize the cultivation conditions for the second stage of clonal micropropagation of Thymus caucasicus Willd. and Thymus serpullum L. Stem segments with one node (8…10 mm), obtained by microcutting of shoots, were cultured on 10 different Murashige and Skoog (MS) nutrient media containing 2% sucrose and 0.8% agar-agar, with the addition of kinetin, thidiazuron, benzylaminopurine (BAP), indoleacetic and gibberellic acids. Various culture vessels (jars, flasks, test tubes) were used for micropropagation. The duration of the cultivation cycle varied from 40 to 70 days. The highest reproduction coefficient of T. serpyllum was noted on the MS medium containing 1.0 mg/l BAP and was 6.7, while that of T. caucasicus was on the MS medium containing 1.0 mg/l kinetin (16.1). The highest efficiency of culturing both thyme species was achieved in jars, with the use of which the reproduction coefficient was 1.4…2.1 times higher than when grown in test tubes or flasks. It is advisable to cultivate the studied thyme species with a standard cycle of 40 days. The best combinations of various thyme reproduction factors contributed to the maximum manifestation of the morphogenetic potential in in vitro experiments. The greatest influence on the multiplication coefficient was exerted by the type of culture vessel, the interaction of the composition of the nutrient medium and the genotype, as well as the composition of the nutrient medium (the shares of the influence of factors ranged from 20.0% to 25.3%). The results of the studies served as the basis for the development of a protocol that can be used for accelerated micropropagation of T. caucasicus and T. serpullum.