Marrubium L., is a problematic genus of Lamiaceae family with approximately 40 taxa that some of its species grow in Iran. In the current study, we studied infrageneric taxonomic relationships among six Iranian Marrubium species using morphological and anatomical traits, and molecular genetic techniques, including inter simple sequence repeats (ISSR), chloroplast DNA (cpDNA) and nuclear ribosomal internal transcribed spacer (ITS). We investigated five individuals per each species. Most of the studied qualitative and quantitative morphological characteristics differed significantly (P ≤ 0.001) among these species, and we found five morphotype groups in the PCA plot of morphological traits. Leaf blade anatomical structure was dorsi-ventral in all species. Meanwhile, we observed a significant variation in most of the studied anatomical variables. Based on anatomical features, these species were clustered into three groups. Results of ISSR study revealed that the total genetic diversity at the species level (Ht) was higher than within each species (Hs). These findings were supported by the results of AMOVA test, Gst and Nm values. According to STRUCTURE analysis and Nei's genetic distance, these species were divided into 5 genotype groups. The studied species were clustered separately in cpDNA and ITS trees of phylogenetic studies. We observed a high level of infraspecific divergence in the evaluated species. In addition, the employed taxonomical markers have enough potential to separate the investigated species. However, the clustering patterns of the species based on the examined techniques were not the same, except those for M. parviflorum Fisch. & C.A. Mey., and M. crassidens Bioss., that were clustered closely in most cases. It can be concluded that the evaluated species revealed a taxonomically complex group resulting from high infraspecific variation, polyploidy and hybridization.
