Genetic diversity is crucial for crop improvement in any breeding program. Cowpea is an important indigenous grain vegetable legume crop. The crop has a significant potential to improve food and nutritional security in sub-Saharan Africa (SSA), and family income for resource poor famers. Cowpea is a source of proteins, vitamins (folate, thiamine and vitamin C), minerals (Fe, Zn, Mn and Ca) and amino acids such as lysine and tryptophan, hence, has a high potential for combating nutrient deficiencies. The SSA countries, including South Africa, have been experiencing many dry seasons, which have negatively affected agricultural production and productivity. Cowpea has a long taproot with the ability to grow in arid and semi-arid regions; however, lasting exposure to severe droughts will result in significant yield and grain quality reduction. There has been limited progress in drought tolerance research in cowpea due to the complexity of this trait, as it involves numerous genes, which in turn are affected by environmental conditions. It is therefore important to review research done on the nutritional, phenotypic and genotypic diversity of cowpea and the importance of diversity when breeding for complex quantitative traits such as drought tolerance and yield. The review will also outline the important omics tools used for drought tolerance breeding, cultivar development and as reference for future cowpea breeding.