Echinophora cinerea Boiss. is an vulnerable plant species which is applied as gastrointestinal invigorator and stimulants in traditional medicine. A study was done to investigate the variation of essential oil (EO) composition of this species among seven wild populations distributed in various microclimates of Zagros Mountain, Iran. Based on the gas chromatography analyses, twenty-one constituents were monitored including 98.6–99.2% of the EO compositions. The major chemical components of essential oils were α-phellandrene (23.7–36.2%), α-pinene (9.5–24.8%), β-myrcene (3.3–17.5%), linalool (1.8–6.7%), β-phellandrene (3.4–5.5%), methyl eugenol (1.1–15.1%), citronellol (0.5–6.4%) and verbenone (1.9–4.9%). Classification of populations revealed four main chemotypes. There were a positive and significant correlation between soil organic carbon and α-terpineol and a negative correlation between α-phellandrene and β-phellandrene contents and the soil EC. The observed variability among the studied populations can provide the best source of materials with favorable components for industrial uses and pharmaceutical industries.