The progressive drying of agricultural fields is considered one of the biggest challenges of food production in the world. The aim of this research was to investigate the effect of the water stress on morphological traits, H2O2, reduced glutathione (GSH) and ascorbic acid (AsA) contents, the activity of APX, GPX, CAT and SOD enzymes and the gene expression of mitochondrial alternative dehydrogenases (NDA2, NDB2, AOX1a and UCP1), in sensitive (Br84-bijelina) and resistant (H301) soybean cultivars. The samples were taken on 0, 1, 3, 6 and 9 days of the experiment. Under the stress conditions, almost all the morphological traits were decreased in both sensitive and resistant cultivars. Unlike sensitive cultivar, the H2O2 content decreased in tolerant cultivar during the stress period. Contents of GSH and AsA were higher under drought stress conditions compared to non-stress treatment in resistant cultivar unlike the sensitive one. Activities of GPX, APX, SOD and CAT were higher in H301 than those in Br84-bijelina cultivar under drought stress conditions. There was an increase in expression of NDA2, NDB2UCP1 and AOX1a in resistant cultivar compared to sensitive one which indicates ROS scavenging mechanisms of mitochondrial electron transport chain in resistant cultivar act more intensively.