The morphological and essential oil diversity of Stachys lavandulifolia populations from the west and northwest of Iran were evaluated. The results showed a significant difference between the populations for nearly all the evaluated traits. The broadest variation ranges were recorded for the auxiliary shoot length, leaf length in the main branch, and the number of flowers in the inflorescences. Furthermore, cluster analysis divided 13 populations into four separate groups. GC/MS analysis verified the presence of 28 components comprising up to 94/4% of the oils. The dominant constituents were α-pinene (1.07–34.87%), (E)-caryophyllene (0.45–25.99%), germacrene D (3.36–20.61%), Δ-cadinene (2.82–19.90%), bicyclogermacrene (1.72–12.08%) α-terpineol (0–11.86%), α-muurolol (0.31–11.50%), p-cymene (0.67–9.67%), β-elemene (0.63–9.31%), and sabinene (0.32–6.29%). The results revealed that natural habitats and the related geo-climatological cues influenced morphological traits and oil composition. Considering the substantial environmental variations and the broad diversity, there would be a rich selection pool for the traits of interest. The populations are a step forward in the breeding programs for the highlighted essential oil constituents needed by the pharmaceutical and related industries. Furthermore, with the future comparative study of the populations from all Iranian territories and the neighboring countries, we will have a realistic idea of the coming conservational and exploitation programs.