Soil and water salinity limits the production potential of crops in many regions of the world. Due to the prevalent arid and semi-arid climate conditions and prolonged irrigation, it is predicted that Iran will be subjected to progressive salinity in the future. Hence, breeding for salinity tolerance of plants is important. Medicinal plants are one of the most important genetic resources in Iran. This study was conducted to evaluate the effect of salinity stress on morphological, phytochemical and physiological traits in 11 genotypes of ajowan. In addition, four selected populations of ajowan were evaluated based on their essential oil composition and antioxidant capacity. A number of 15 seeds of each ecotype were sown in a 15 Kg pot in Chahanari greenhouse in 2017. The genotypes were grown under different salt concentrations including zero (control), 6, 9, and 12 dSm -1 . The experiment design was a factorial experiment according to a randomized complete design with three replications. The results of analysis of variance showed that salinity stress significantly affected all the measured traits. Morphological traits showed an increase tendency in 6 dSm -1 . Salinity stress was found to increase oil yield in most ajowan populations. The highest oil yield was in Farsmar under 12 dSm -1 (5.27%). The results of GC–MS analysis in 4 ajowan populations revealed that thymol (32.7-54.29), ? -terpinene (21.71-32.81), and p-cymene (18.74-26.16) to be the major compounds. The highest and lowest thymol levels were recorded for Qazvin in control condition and Qazvin under 6 dSm -1 . The highest phenolic and flavonoid contents were detected in Khormo under 12 dSm -1 (189.63 mg TAE g -1 DW) and Yazd under 9 dSm -1 (5.82mg QE g -1 DW), respectively. Moreover, Yazd under 9 dSm -1 exhibited the strongest antioxidant activity based on DPPH (IC 50 =1566.98µg/mL) and Yazd under 12 dSm -1 revealed the highest reducing power (0.69 nm). Salinity stress caused significant increases in hydrogen-peroxide content under 12 dSm -1 and malondialdehyde (MDA) content under 9 and 12 dSm -1 . The highest increase in MDA and H 2 O 2 were obtained in Qazvin in control condition. The salinity treatment resulted in increase in gayacol peroxidase activity under 12 dSm -1 and increased ascorbat peroxidase activity under 6 dSm -1 in the ajowan cultivars. Also, at most ajowan cultivars, protein content increased in salinity stress. The highest increase in gayacol peroxidase, ascorbat peroxidase and protein were in Qazvin (12 dSm -1 ) and Khormo (Control), Rafsanjan (9 dSm -1 ) and Rafsanjan (Control), and Esfahfo (12 dSm -1 ), respectively. Salinity stress resulted in decrease in chlorophyll a, chlorophyll b and carotenoid content in most populations of ajowan. The highest content of chlorophyll a, chlorophyll b and carotenoid was obtained in Ardebil in control condition. The results of principle component analysis (PCA) showed that the three first components justified 61.8, 55.37, 59.24 and 55.84 percent of total variations under normal (control) and salinity stresses of 6, 9 and 12 dSm -1 conditions, respectively. According to cluster analysis, the genotypes were separated into four groups on the basis of phytochemical, physiological and morphological traits under normal and salinity stress of 6, 9 and 12 dSm -1 conditions, respectively. Overall, the results revealed that low and moderate salinity stress (i.e., 6 and 9 dSm -1 ) possibly improved the nutritional value of ajowan, making it especially useful for pharmaceutical and food applications. Key word: Salinity, Morphological, Physiological and phytochemical traits, Essential oil.