The ILRI forage genebank conserves over 691 cowpea (Vigna unguiculata L.) accessions, forming part of the CGIAR collection of more than 16,000 that represent the global largest collection. This collection exhibits extensive genetic and phenotypic diversity, including forage, grain, and dual-purpose types, as well as early maturing, high-protein, and low-fiber accessions. These genetic resources are critical for breeding programs targeting diverse agro-ecologies and water-limited environments. Cowpea is a key legume in Sub-Saharan Africa, valued for its drought tolerance, nutritional benefits, and contribution to soil fertility. In East Africa, particularly Ethiopia, Kenya, Uganda, Tanzania, and Sudan, it serves as a major source of food, income, and livestock feed for smallholder farmers, making it an important climate-smart crop. The collections were genotyped using the DArTseq platform, generating genome-wide high-density SNP and SilicoDArT markers, of which 93% of the SNPs and 83% of the SilicoDArTs were successfully mapped to the V. unguiculata genome. Based on selected genome-wide SNP markers and passport data, a core subset of 102 accessions (20%) capturing the maximum diversity within the ILRI forage genebank collection was identified. This manageable subset can serve as a representative reference set for distribution and evaluation across different agro-ecologies of the world.