More than 1.4 billion people live in the semi-arid tropics, areas in over 55 developing countries that have marginal soils, poor infrastructure, and erratic and low rainfall. The International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) works to improve the agricultural systems of the resource poor farmers in the semi-arid tropics through a major focus on the development of improved crop varieties of sorghum, pearl millet, groundnut, chickpea and pigeonpea. While good progress has been made to improve productivity, stability and nutritional value of these crops, scientists continue to look for options to utilize the full range of natural crop diversity. Under the CGIAR’s Generation Challenge Program, ICRISAT is evaluating the molecular diversity using 20-50 SSRs in 1000-3000 accessions for each of these crops. This information, when coupled with phenotypic information, is allowing a more refined subset of germplasm to be defined that contains the range of diversity expected in the full collection, and which can be assessed for breeding against a range of biotic and abiotic stresses. The genotypic information also provides an excellent opportunity to assess other germplasm collections in relation to the global collection held in ICRISAT’s gene bank. Wild species also provide unique opportunities to enhance the resistance in cultivated varieties to insect pests (e.g., pod borers in chickpea and pigeonpea) and diseases (e.g., leaf spots, bud and stem necrosis in groundnut; sterility mosaic in pigeonpea), as well as identifying male sterility systems useful in developing hybrids (e.g., in pigeonpea). By linking genetic resources with modern molecular genomics, the speed at which novel and useful genes (alleles) can be identified and introgressed into varieties is being increased. This approach is forming an important basis for our current and future breeding efforts to provide improved crop varieties to farmers in the semi-arid tropics.