Stachys lavandulifolia is an herb growing wild in Iran with interesting medicinal properties. In this research, the variability of morphological characters and phytochemical compositions among and within eight populations of this species was studied. Characteristics including inflorescence length, internode length, leaf shape, corolla color, state of calyx trichomes, state of leaf trichomes and corolla length were the most variable morphological characteristics among the examined populations. The phytochemical characterization revealed 45 components in the essential oils. Germacrene D and δ-cadinene were the main component with the highest contents. α-Copaene was positively correlated with δ-cadinene and limonene, while germacrene D was negatively correlated with δ-cadinene. UPGMA dendrogram constructed based on combined data of morphological variables and phytochemical compositions distinguished studied populations with high inter- and intra-population diversity. The high level of phytochemical and morphological variability among and within the studied populations suggests a breeding approach during the domestication, to gain new, promising, and homogenous cultivars, attractive for the industry and agriculture.