Rust is one of the three major diseases in cowpea. Developing rust resistance cultivars is the most cost-effective strategy to scab this disease, and digging the resistant germplasm and elucidating the genetic basis of rust resistance is the key and prerequisite for cowpea rust resistance breeding. In the current study, 215 cowpea landraces were precisely evaluated for rust resistance and 40 accessions with nearly immune phenotype to rust were identified. Through resequencing the 215 accessions, 3880169 high quality SNPs and 469398 high quality InDels were identified. Total of 10 genomic regions significantly associated with rust resistance were detected by GWAS, and haplotype analysis based on the peak SNP of each signal showed that their alleles variation were highly correlated to rust phenotypes, the resistance accession ratio increased significantly along with the pyramidingmore and more favored alleles in a single accession. Ten predicated genes were identified as the candidate genes for the ten GWAS signals, including BTB/POZ domain-containing protein, LRR receptor-like serine/threonine-protein kinase, ethylene-responsive transcription factor and alternative oxidase genes.. These results will providethe theoretical guidance and gene resources for molecular breeding of rust resistance in cowpea.