Cowpea is an important legume crop in West Africa, providing a valuable source of protein and income for millions of people. However, despite its importance, there is limited knowledge about the genetic diversity of cowpea cultivars in the region. This study aimed to investigate the genetic diversity of sixty cowpea cultivars from Benin, Ghana, and Nigeria using both morphological and molecular characterization methods. The cultivars were evaluated for 38 agro-morphological traits and genetically characterized using AFLP markers. Results revealed a significant degree of genetic diversity among the cultivars, with wide variation in both quantitative and qualitative traits. Two major clusters were identified in the West African cowpea germplasm, indicating the existence of two different gene pools. Genetic relatedness did not seem to depend on the geographical origin of the cultivar, suggesting extensive movement and adaptation of cowpea genetic materials across the West African sub-region. The study demonstrates the importance of characterizing genetic diversity to aid in breeding and improving cowpea cultivars for desirable traits such as time of maturity, photoperiod sensitivity, plant type, seed quality, and resistance to major diseases, insect pests, or parasites. This research contributes to the conservation and utilization of cowpea genetic resources and highlights the need for continued efforts to preserve and improve the genetic diversity of this important crop