This study uses numerical methods to describe, illustrate and assess the taxonomic significance of morphological and anatomical features of Scrophularia ilwensis C. Koch, S. capillaris Boiss. & Ball., S. nodosa L., S. libanotica Boiss. var. pontica R. Mill, S. lucida L. and S. cinerascens Boiss. collected from NE Anatolia. Features related to peculiarities of the leaf, bracteole, alar pedicel and corolla were found to be important in separating the taxa morphologically, but principal component analysis of all characters showed some anatomical characters (mean number of stomata, diameter of vascular bundle and scleranchymatic sheath) to be more important than morphological ones in explaining the variation between the examined taxa.