Salvia limbata is a medicinal plant of the Lamiaceae family that is naturally distributed in various regions of Iran and neighboring countries. In the current evaluation, the leaf blade and petiole anatomical variables were examined in eight Iranian S. limbata populations to explore their taxonomic significance and interpopulation variations. The evaluated populations were harvested from three subprovinces of the Irano-Turanian province. The plant samples were fixed in formaldehyde 90%, ethanol 5%, acetic acid 5% solution, and the hand cross sections of the blade and petiole were double stained with carmine and methylene blue. Data were analyzed using PAST ver. 2.1 and findings revealed that all qualitative variables were invariable between populations, except for the shape of the leaf blade and the epidermal cells of the petiole. Most quantitative traits varied among the considered populations by principal component analysis (PCA) and divided the investigated characteristics into seven components, where two first components had more than 80% of the total variation. In PCA loading, most of the characteristics assessed were negatively correlated. According to UPGMA dendrogram and PCA plot, the populations were clustered into three groups. The PCA biplot revealed the distinct characteristic(s) for each classified group. The clustering patterns of these populations were not in agreement with the geographical distance and phytogeographic similarity between the populations. Several anatomical characteristics were found similar to those recorded in some Lamiaceae genera and lacked taxonomic value, whereas others had taxonomic importance at the infraspecific level. According to a phytogeographic survey and a previous study of molecular genetic diversity, it can be suggested that genetic background can create enough anatomical adaption in populations of S. limbata to establish itself in a wide range of habitats. Meanwhile, the microhabitat has a powerful influence on the anatomical structure.