In the current study, we evaluated the morphological and genetic diversity among Iranian populations of Marrubium parviflorum Russel and Marrubium cuneatum Fisch. & Mey. Both species are naturally distributed in various parts of the country, and are morphologically very similar. In total, we evaluated 16 populations of these species. For morphology, we studied the quantitative and qualitative characteristics of both reproductive and vegetative organs. For molecular investigation, the nuclear genomic was extracted using modified CTAB method and amplified using several ISSR molecular primers. Data were analyzed using SPSS ver. 16, PAST, GenAlex 6.4, STRUCTURE, Geno–Dive ver.2, and PopART. In both species, most of the quantitative morphological characteristics varied significantly among the populations. Moreover, most of the qualitative ones differed among and within the populations. Parameters of genetic diversity and polymorphism differed among the populations of both species. In M. parviflorum, the great proportion of significant genetic difference belonged to within populations, while, the reverse conditions were found in M. cuneatum populations. Strong population genetic differentiation existed in M. cuneatum, which was supported by a flat rate of gene flow. Meanwhile, the occurrence of a high rate of gene flow leads to a weak population genetic differentiation in M. parviflorum. However, the populations of both species were mixed together in morphological and ISSR dendrograms, which revealed similarity among these species. It seems that the occurrence of ancestral gene flow or recent speciation were responsible for these similarities.
