The genus Iris is an economically and ornamentally important genus in the family Iridaceae. Root and leaf anatomy have great potential to aid with species identification and clarify taxonomy of plant species within the family. Iris subgen. Scorpiris are a taxonomically difficult group due to morphological character variation and overlapping geographical distribution. Thus, additional morphological characters need to be articulated for correct identification and to define species boundaries in the group. Here, we studied root (nine characters) and leaf (10 characters) anatomical traits of seven species in the Iris subgen. Scorpiris in detail to evaluate their taxonomic value. Significant variation was found in the transverse section of the root (i.e. exodermis, cortex cells, endodermis, pericycle, xylem and phloem) but not in leaf anatomy. Hence, root anatomical traits can be used as additional characters for correct identification of species within the Iris subgen. Scorpiris. Box plots, principal component analyses and one-way analysis of variance were performed using quantitative characters for the studied species. Our results demonstrate that the number of exodermis layers, protoxylem and metaxylem numbers in the roots are of phylogenetic value in the studied species.