Ducrosia anethifolia (DC.) Boiss. is an aromatic medicinal plant that has been traditionally used as an analgesic to treat headaches, backaches, colic, and cold. This study evaluated the yield, physiological, and phytochemical traits of 24 populations for 2 consecutive years under the water stress condition. The seed yield and physiological traits demonstrated the highest values in the first and second year, respectively. Hydrogen peroxide (HO), proline, malondialdehyde (MDA), and antioxidant activity enzymes were elevated, while chlorophyll, carotenoids, relative water content (RWC), and yield decreased under drought stress. High-performance liquid chromatography (HPLC) was also applied to assess the changes in some polyphenolic compounds in response to water stress. The increase in some phenolic compounds, such as p-coumaric acid, was recorded due to drought stress, while there was a decrease in flavonoids, that is luteolin and quercetin. Among the populations, Abarkuh2 indicated the highest increase in p-coumaric acid (96%) in response to drought stress. In general, high diversity among the studied populations provides new insights into choosing the beneficial populations for medicinal and food purposes. HIGHLIGHTS: • Changes in polyphenolics of Moshgak populations were obtained in response to water stress. • Gallic acid, ferulic acid, p-coumaric acid and vanillic acid were the major components. • The phenolic compounds was increased due to drought stress while flavonoids were decreased High variation was obtained between Moshgak populations.