Bean rust is a devastating disease of common bean in the Americas and Africa. The historically important Ur-3 gene confers resistance to many races of the highly variable bean rust pathogen that overcome all known rust resistance genes. Existing molecular markers tagging Ur-3 for use in marker assisted selection produce false results. We described here the fine mapping of Ur-3 for the development of highly accurate markers linked to this gene. An F2 population from Pinto 114 × Aurora was evaluated for its reaction to four different races of the bean rust pathogen. A bulked segregant analysis using the SNP chip BARCBEAN6K_3 positioned the approximate location of the Ur-3 locus to the lower arm of chromosome Pv11. Specific SSR and SNP markers and haplotype analysis of 18 sequenced bean lines led to position the Ur-3 locus to a 46.5 Kb genomic region. We discovered a KASP marker, SS68 that was tightly linked to the Ur-3 locus. Validation of SS68 on a panel of 130 diverse common bean lines and varieties containing all known rust resistance genes revealed that it was highly accurate producing no false results. The SS68 marker will be of great value to pyramid Ur-3 with other rust resistance genes. It will also reduce significantly time and labor associated with the current phenotypic detection of Ur-3. This is the first utilization of fine mapping to discover markers linked to a rust resistance in common bean.