Mean performance and genetic variability were assessed in four soybean genotypes and their F1 crosses using phenotypic data and SRAP markers under drought stress conditions. The results showed that mean squares of G x E interaction were found to be highly significant for most studied traits. Also, the mean performances of four parents and their 6 crosses were variable from normal irrigation to drought stress condition. It could be observed that the parent genotype P2 were relatively stress tolerant parent with the DSI value of 0.5. Using SRAP markers, a total of 49 bands were amplified, of which 24 bands (48.98%) were found polymorphic. Furthermore, the polymorphic band numbers ranged from 2 to 6 bands. The percentage of polymorphism (%P) ranged from 40% (ME2-EM10 primers) to 62% (ME7-EM6 primers) with an average of 48.85%. The SRAP marker ME5-EM1590bp was regarded probably as candidate marker which linked to plant height trait. Interestingly, three different markers (ME1-EM6950bp, EM4-ME61000bp and EM7-ME6970bp) were regarded as candidate markers linked to number of branches per plant. The results showed highly significant and significant regressions (0.3249**, P= 0.013) and (45.04*, P= 0.053) on number of branches per plant and plant height traits, respectively. The UPGMA cluster analysis based on the SRAP markers and the means of morphological traits separated the soybean parental genotypes into two significantly different clusters. Finally, the correlation between the two markers is not significant (r = 0.565, P=0.932).