Genetic resistance to Uromyces appendiculatus, the rust pathogen of common bean, is conferred by single and dominant genes. Gene pyramiding is essential to manage the extensive and shifting virulence diversity of U. appendiculatus. However, the pyramiding of genes exhibiting epistasis is difficult. Alas, epistasis is frequent among rust resistance genes of common bean. In epistasis, one gene (epistatic) masks the presence of another gene (hypostatic) and prevents the identification of the masked genes. In this study, we wanted to investigate the presumed epistasis between Ur-3 and Ur-5 genes that have been used extensively in breeding programs. Ur-3 confers resistance to 55 and Ur-5 to 73 of 94, races of U. appendiculatus. The resistance reactions of Ur-3 and Ur-5 are hypersensitive spots and tiny pustules, respectively. We used an F₂ population from a cross between common bean cultivars Aurora (with Ur-3) and Mexico 309 (with Ur-5), four specific races of the rust pathogen, and the new SS68 and SS183 KASP markers developed using high-throughput genotyping and sequencing technologies. Inoculation of the F₂ plants with the rust pathogen races revealed a 12:3:1 phenotypic segregation ratio (hypersensitive spots: tiny pustules: large pustules), indicating that Ur-3 was epistatic to Ur-5. The SS68 and SS183 markers that were tightly linked to Ur-3 and Ur-5 respectively, also established that Ur-3 was epistatic to Ur-5. In addition, these markers will facilitate and speed up the development of dry and snap bean cultivars combining Ur-3 and Ur-5 with other rust resistance genes.