In domestication and improvement of plants, information on genetic variations of different population can be helpful in recognition of genetic structures and relations between populations. It also can be helpful in selection of domestication process. Scarcity of water is a severe environmental constraint to plant productivity. Drought- induced loss in crop yield probably exceeds losses from all other causes, since both the severity and duration of the stress are critical. Cumin is one of the drought tolerance medicinal plants of Iran which can grow in most regions of the country. Despite of its importance, limited breeding work has been done to asses cumin germplasm for drought tolerance. This study was conducted to investigate the genetic variation in Iranian cumin germplasm under normal and water deficient conditions. Traits such as number of days to 50% emergence, number of days to 50% flowering, seed yield and it’s components, biological yield, harvest index, relative water content (RWC), proline and photosynthetic pigments were evaluated. In total 93 genotypes were studies in this experiment. The field experiment was carried out according to a randomized complete block design with two replications for each environments. The results of analysis of variance for normal condition showed significant genetic variation for seed yield and it’s components and all of studied physiological traits between the genotypes. Drought stress had significant effects on agronomical and physiological traits. The heritability of traits was estimated to be more than 50% and indicated that most of this variation are due to genetic effects. Amongst agronomical traits, number of seeds per umble and seed yield at two moisture conditions had the most variation. Among physiological traits, proline and carotenoid content at the two conditions had the most variation. Drought stress had a significant effect on all of agronomical traits except for the number of days to 50% emergence and days to 50% flowering. Drought also effected all of the physiological aspects expect chlorophyll a to b ratio. There was positive correlation between umbel per plant and seed yield. Among all yield components, umble per plant and seed per umble had the most correlation. There was negative correlation between days to 50% flowering and umble per plant. At drought stress, correlation between RWC and seed yield was the highest. At both moisture conditions, stepwise regression results revealed, that umbel per plant defined most of the variation for yield and can be used as an index for selection. Factor Analysis, for all traits under two moisture conditions, showed five hidden factors which justified more than 72% of all variations. Principle component results for both moisture levels characterized the genotypes into six major groups inconsistence with geographical distribution of germplasm. Based on the first two principle components, at both moisture conditions, biological yield and harvest index and at drought stress condition relative water content of leaf were good characteristics for indirect selection of seed yield. Results indicates that STI,GMP and MP are effective selection criterion for identification of tolerant genotypes. Based on these indices genotype 92 and 93 were the most tolerant genotypes. Based on conducted principle component for tolerance indices, first two factors defined more than 96% of variations. The first PC was named performance potential and the second PC was named sensitivity. Based on the PCA, genotypes were divided into three groups including tolerant, semi tolerant and sensitive to drought Key words : Cumin, Genetic Variation, Drought Stress, Drought Toleration Index