The medicinal genus Salvia L. belongs to Lamiaceae family with more than 900 species worldwide. It is a very variable and taxonomically difficult genus. This genus has two important centers of diversity viz Asia and Mediterranean area. This investigation used anatomical traits to find distinguishable characters between the Salvia species distributed in Northeast of Iran. For anatomy study, cross sections of peduncle and petiole were prepared by hand using razor blade and stained by Safranin and Fast green. In this investigation we studied petiole and stem anatomy of 18 taxa of Salvia species from northeastern Iran to determine valuable anatomical characters. Principal Component Analysis and Cluster analysis were used for statistical studies. The result of this study showed that some characters such as collenchyma layer in peduncle, shape of petiole, presence of collenchyma in peduncle and petiole shape of xylem seem to be used as the discriminating characters.