Despite the importance of drought stress in early stage of growth and plant establishment, it has usually been neglected as selection criteria in breeding programs. Therefore, a population of recombinant inbred line derived from the cross “Babax/Seri M82” and their two parents were studied. The experiment was conducted in two randomized complete block designs with two replications under osmotic (-8 MPa) and non-osmotic stress conditions in 2012. Germination percentage, promptness index, shoot and root length and their proportion, shoot and root fresh weight, shoot and root dry weight, number of root, seed vigor, water soluble carbohydrate, relative water content and germination stress index were measured. QTL analysis was conducted by composite interval mapping method separately for each trait under each condition and mean of two conditions. A molecular genetic linkage map including 249 AFLP, 74 SSR and 264 DArT markers was used for QTL analysis. Based on combined analysis of variance, the main effect of genotype was highly significant for all studied traits and transgressive segregation in both directions (positive and negative) was observed. Thirty four QTLs were found for the studied traits. Phenotypic variation that were explained by these QTLs, varied from 15.86-28.81%. The highest and the lowest phenotypic variations were related to RWC and GSI. QTL of 25.20 cM location of chromosome 1B, controlling RWC, was quite stable, therefore, may be used in marker assisted selection. MAS for RWC may enhance the plants' ability to maintain the growth of them in drought-prone soils at the critical early developmental stages.