Marrubium parviforum Fisch. & C.A. Mey. and Marrubium cuneatum Russell, are naturally distributed in various parts of Iran. It is difcult to clearly identify these species, because of their morphological similarities. Therefore, in the current study, we investigated the morphological characteristics and genetic diversity among various populations of these species in the country to fnd more variable traits and compare their genetic structure. In total, we evaluated 16 populations of these species, with up to ten replications per each population. For morphology, we studied the quantitative and qualitative characteristics of both reproductive and vegetative organs. For molecular investigations, the nuclear DNA was extracted using modifed CTAB method and amplifed using twelve ISSR molecular primers. Data were analyzed using SPSS, PAST, GenAlex, STRU CTURE, and Geno–Dive. Results indicated that in both species, most of the quantitative and qualitative morphological characteristics varied among and within the populations. Parameters of genetic diversity and polymorphism difered among the populations of both species. According to AMOVA test,
