Cowpea is one of the most important legume crops worldwide， serving not only as an important coarse cereal but also as a traditional vegetable in China. Rust is one of the three major diseases in cowpea， and developing rust resistance cultivars is the most cost-effective strategy in disease control. Exploring 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 examined for rust resistance and 40 accessions showing resistance to rust were identified. Through resequencing the 215 accessions， 3880169 high-quality SNPs and 469398 high-quality InDels were found. These accessions were divided into four subgroups through population structural analysis， and the subgroup division was highly related to pod length and pod type. Total of 10 genomic regions， which significantly associated with rust resistance and distributed on seven chromosomes， were detected by GWAS. Haplotype analysis based on the associated SNPs showed that their alleles were highly correlated to rust resistance. The ratio of resistance accessions increased significantly， when pyramiding increasing number of favored alleles. Ten candidate genes were identified， including BTB/POZ domain-containing protein， LRR receptor-like serine/threonine-protein kinase， ethylene-responsive transcription factor and alternative oxidase genes. These results will provide the theoretical guidance and gene resources for molecular breeding of rust resistance in cowpea.