Rust disease, incited by the fungus Uromyces vignae, adversely affects production and quality of asparagus bean and other types of cowpea in many parts of the world. Genetic resistance to the rust pathogen has been identified in a few accessions, but it is difficult to efficiently transfer the resistance to a broad range of asparagus bean cultivars using traditional breeding approaches. We determined that rust resistance was controlled by a single dominant gene designated Rr1 in the cross of a highly resistant cultivar ZN016 and highly susceptible cultivar Zhijiang 282. Bulked segregant analysis was applied to an F2 population derived from these parents, and an AFLP marker (E-AAG/M-CTG), 150 bp in size, was detected in the resistant bulk. The AFLP fragment was then converted to a SCAR marker, named ABRSAAG/CTG98, and the genetic distance between the marker and the Rr1 gene was estimated to be 5.4 cM. This SCAR marker could be used effectively for MAS of Rr1 in breeding programs to develop rust-resistant asparagus bean cultivars and potentially more widely to breed rust-resistant cultivars of other types of cowpea.