The aim of this study was to determine the variations among cephalic plates of individuals in two populations of Clinopodes flavidus in Alborz Mountains, by means of landmark-based techniques of geometric morphometrics. Therefore, 17 landmarks and semi-landmarks on the coxosternite of poison claw and seven landmarks and semi-landmarks on the tarsangulum of poison claw were selected using TpsDig2 software. Data of landmarks, after procrust analysis, were subjected to various multivariate analyses, such as Principle Component Analysis (PCA) and Canonical Variate Analysis (CVA) by means of PAST and MorphoJ softwares. The results obtained demonstrated that shape variations in coxosternite were significantly different among various populations (p<0.001). This study revealed the usefulness of landmark-based geometric morphometrics in the differentiation of various populations of Clinopodes flavidus in Alborz Mountains.