Soybean is an oilseed legume that plays a vital role in sustainable agriculture through the biological fixation of atmospheric nitrogen. However, global warming is currently worsening the drought stress on which productivity depends. In this scenario, marker-assisted breeding (MAB) is an appealing tool for improving tolerance against water-deficit condition in soybean by detecting and incorporating favourable alleles into elite cultivars. This chapter discusses the impacts of drought stress on the sustainability of soybean under the changing climate. This chapter also explores advanced techniques for enhancing the soybean plants’ ability to withstand drought. This chapter primarily focuses on the recognition of genetic markers that are linked to drought tolerance features using QTL and association mappings and genomic selection, utilising advanced molecular methods. This chapter also searches the significance of genomics to accelerate the development of drought-tolerant soybean cultivars that can be integrated with conventional breeding approaches. Moreover, this chapter discusses the limitations and potential of using MAB to enhance water stress tolerance in breeding programmes. Due to the multigenic nature of drought resistance, a mixed selective strategy is important for designing new soybean varieties with high yield stability under water-limited conditions. Molecular genetics and genomics provide significant opportunities for MAS, which can increase the rate of drought-tolerant soybean development for better food security and economic sustainability under current unpredictable climatic conditions.