Nepeta viscida and N. nuda subsp. nuda and N. × tmolea were examined in this study. Mainly fresh leaf pieces, dried with silica grains, were used for DNA extraction procedures via DNA isolation kits. Standard PCR techniques were executed using three different primer sets (one nuclear DNA region (nrITS) and two chloroplast DNA regions (rpl32-trnL and trnA(Leu)-trnA(Phe)-trnL-F). DNA sequences were analysed and evaluated using different molecular approaches and software. Consequently, the inconstant molecular structure and hybrid nature of N. × tmolea specimens were shown and interpreted in this study. According to our result, N. × tmolea have some intermediate characters compared to its parents. nrITS data give more information phylogenetically, and also the most polymorphic loci are seen in nrITS data. Morphological and molecular data contribute to define separation of N. × tmolea. Consequently, the inconstant molecular structure and hybrid nature of N. × tmolea specimens were shown and interpreted in this study.