The aim of this study was to molecularly identify and assess the genetic diversity of 12Mentha genotypes using, for the first time, two types of DNA markers simultaneously –ISSR (inter simple sequence repeats) and SCoT (start codon targeted). Selected genotypes representing various Menthaspecies and varieties were analyzed to determine the level of genetic similarity and phylogenetic relationships between them. The level of polymorphism obtained for ISSR markers was 71%, while for SCoT it was 88.7%. The obtained data were analyzed, allowing for the assess-ment of the level of genetic similarity and the construction of dendrograms illustrating the genetic structure of the studied population. Studies indicate that the use of SCoT markers enables the iden-tification of the following genotypes: Plectranthus amboinicus(Lour.) Spreng, Mentha pulegiumL., Mentha spicataL. cv. Moroccan, Mentha suaveolensEhrh. var. variegata(pineapple mint), Mentha spicataL., and Mentha longifolia L. ISSR markers, due to the generation of only monomorphic and polymorphic bands, do not allow for the direct identification of any of the studied genotypes. Data from both marker systems indicate significant genetic diversity among the analyzedgenotypes, which may be important for breeding programs and the conservation of genetic resources of the Mentha genus.