Sixteen taxa of Ballota were investigated by analyzing the contents of diterpenoid and flavonoid compositions, and the relationships were compared with their morphological properties. HPLC chromatograms of diterpenoids and flavonoids from acetone extracts of sixteen Ballota taxa revealed the presence of thirteen compounds. Isolated compounds from Ballota species were evaluated by the unweighted pair-group arithmetic average (UPGMA) clustering method. B. glandulosissima is distinct from all other taxa in the dendogram, and this species is morphologically different from other taxa by having a high number of glandular hairs. The second group is composed of B. saxatilis ssp. saxatilis and B. inaequidens; these two species are in close kinship as evidenced by their morphology (similar calyx shape). In the latter clusters at most, the affinities among taxa, as suggested by diterpenoid and flavonoid pattern, are only partially congruent with affinities based on other evidence. In general, morphologic, anatomic characters, distributions, and habitats are not concordant with the clusters. Also, no concordance was found between the sections, phylogenetic order , and those of the groups formed by cluster analyses.