It is critical to identify crops with an acceptable yield under low-input conditions, which are also tolerant to water shortage and could maintain good soil quality. Therefore, this study was carried out in soil columns to investigate the effect of cultivated and wild safflower genotypes and their selected generations on some soil physical and chemical properties [i.e., dispersible clay content, water repellency, structural stability indices of high energy moisture characteristic (HEMC), organic carbon content, percent of water stable aggregates, basal microbial respiration and total nitrogen] in soil columns under drought stress treatments in outdoor condition. Drought stress treatments were applied based on maximum allowable depletion (MAD) including mild stress (MAD of 50%), moderate stress (MAD of 70%) and severe stress (MAD of 90%). Nine safflower genotypes including one cultivated genotypes, two wild ones and six genotypes as their generations were used. Plant morphological, physiological and root characteristics were studied in the experimental treatments as well. The experiment was conducted in a factorial arrangement of treatments in completely randomized design with three replicates in hydro-flume. After eight months, the plants were harvested, and soils and roots were extracted for further analyses. The results showed that wild genotype Belong to the species of Carthamus oxyacanthus had the highest number of seeds per capitulum. The cultivated genotype C. tinctorius (C111) in the severe stress level had the lowest leaf water potential but genotypes of C. palestinus and F2cp had lower resistance to drought stress. Drought stress significantly increased the leaf proline content. The wild genotype C. oxyacanthus had the highest proline content. Greatest mean values of root surface area (i.e., 0.71 m 2 /m 3 soil) and root length density (i.e., 89.9 m/m 3 soil) were observed in this genotype as well. However, the lowest mean values of root surface area and length density (i.e., 0.45 m 2 /m 3 and 50.4 m/m 3 , respectively) were observed in genotype F4co. Dry weight of root was highest at the moderate stress level but decreased to its lowest value at the severe stress. The highest ratio of dry shoot weight to root weight was observed in the moderate stress. Mean comparisons of soil organic carbon content among the drought stress levels showed that the highest organic carbon content in the rhizosphere was measured in the moderate stress level presumably due to greater root exudates. The highest soil basal microbial respiration was measured in the moderate stress level. The water stress increased the soil carbohydrates so that they were significantly greater in the moderate and severe stress levels compared to the mild stress level. Genotype, drought stress and their interaction did not significantly affect the soil water repellency index and related parameters. Similarity of HEMC curves of fast and slow wetting conditions for the rhizosphere soil of wild genotype C. oxyacanthus was higher in the moderate stress condition compared to mild and severe stress levels. This finding indicated greater soil structural stability under the moderate stress level. Considering the marginal soils characteristic to arid and semi-arid regions in Iran, adopting safflower genotypes capable of improving soil quality attributes along with producing an acceptable grain yield must be taken into account in future studies; parent genotypes of safflower ( C. tinctorius , C. oxyacanthus and C. palestinus ) might be suitable in this regard based on the current study results. Keywords Soil structural stability, Root exudates, Drought stress, High energy moisture characteristic curve, Wild and cultivated safflower, Organic carbon.