<p>Cowpea (<i>Vigna unguiculata</i> (L.) Walp.) is the most important grain legume in sub-Saharan Africa where it provides a significant source of human nutrition and animal fodder to millions of low-input farmers. While adapted to a wide range of soils and generally considered climate resilient due to its drought and heat tolerance, cowpea yields are suboptimal throughout its main growing region because of numerous abiotic and biotic stress factors and low soil fertility. Among the major limitations is low available soil phosphorus (P) and, therefore, improving cowpea cultivars for growth under limiting P conditions would be of great importance and benefit to local low-input farmers. We grew a multi-parent advanced generation inter-cross (MAGIC) population of cowpea consisting of 305 F₈ recombinant inbred lines (RILs) generated from eight genetically diverse founder parents and phenotyped them for root system, shoot system, and total biomass production under normal and low phosphate conditions in an ebb and flow hydroponic system. We then performed a genome wide association study (GWAS) to identify genes associated with phosphorus use efficiency (PUE). Two SNPs were identified that are significantly associated with shoot system growth under phosphate stress: one located on chromosome Vu09 and the other on Vu10. A third SNP was identified on Vu03 that is associated with enhanced root production under phosphate stress. Characterizing the underlying genetic basis for PUE can assist in the improvement of cowpea for better productivity across Africa.</p>