Cowpea [Vigna unguiculata (L.) Walp.] is a diploid and nutrient-dense legume species. It provides affordable source of protein to human. Cowpea cultivation is prevalent in Africa, Asia, the western and southern U.S., and Central and South America. However, earlier reports have shown that drought and salt stress can be devastating to cowpea production. The objectives of this study were to screen for salt and drought tolerance in cowpea and to identify molecular markers associated with these traits. Simple methodologies to screen for drought (Chapter 2) and salt tolerance were developed (Chapter 3). Results suggested that: 1) a total of 14, 18, 5, 5, and 35 SNPs were associated with plant growth habit change due to drought stress, drought tolerance index for maturity, flowering time, 100-seed weight, and grain yield respectively in a MAGIC cowpea population, the network-guided approach revealed clear interactions between the loci associated with the drought tolerance traits, and GS accuracy varied from low to moderate for this population, 2) a total of 7, 2, 18, 18, 3, 2, 5, 1, and 23 SNPs were associated with various traits evaluated for salt tolerance in a MAGIC cowpea population, some of these SNPs were in the vicinity of potassium channel and biomolecule transporters, and significant epistatic interactions were found 3) a large variation of salt tolerance and drought tolerance was found in the panel involving 331 cowpea genotypes which were genotyped with 14,465,516 SNPs obtained from whole-genome resequencing, 4) tolerance to salt and drought-related traits seemed to be associated with the geographical origins of the cowpea genotypes, 5) a significant GWAS peak defined by a cluster of 196 significant SNPs and mapped on a 210-kb region of chromosome 5 was identified to be a good locus candidate for tolerance to trifoliate leaf chlorosis under drought stress in cowpea and harbored hormone-induced genes, and 6) a strong candidate locus for tolerance to leaf score injury under salt stress and defined by a cluster of 1,400 significant SNPs on chromosome 3 was identified and this region harbored a potassium channel gene. The results from this study could contribute to a better understanding of salt and drought tolerance in cowpea. The salt- and drought-tolerant genotypes could be used as parents in cowpea breeding programs.