(BCMV) is a major disease in common bean ( L.). Host plant resistance is the most effective strategy to minimize crop damage against BCMV and the related (BCMNV). To facilitate breeding for resistance, we sought to identify candidate genes and develop markers for the gene and the unknown gene with which it interacts. Genome-wide association study (GWAS) of the Durango Diversity Panel (DDP) identified a peak region for on chromosome Pv11. Haplotype mapping narrowed the genomic interval and identified Phvul.011G092700, a vacuolar protein-sorting 4 (Vps4) AAA+ ATPase endosomal sorting complexes required for transport (ESCRT) protein, as the candidate gene. The race Durango Phvul.011G092700 gene model, , contains a 10-kb deletion, while the race Mesoamerican consists of a single nucleotide polymorphism (SNP) deletion. Each mutation introduces a premature stop codon, and they exhibit the same interaction with the pathogroups (PGs) tested. Phvul.005G125100, another Vps4 AAA+ ATPase ESCRT protein, was identified as the candidate gene for the new recessive gene, and the recessive allele is likely an amino acid substitution in the microtubule interacting and transport (MIT) domain. The two Vps4 AAA+ ATPase ESCRT proteins exhibit high similarity to the Cucsa.385040 candidate gene associated with recessive resistance to in cucumber. alone has no resistance effect but, when combined with , provides resistance to BCMV (except PG-V) but not BCMNV, and, when combined with , provides resistance to BCMV (except BCMV PG-VII) and BCMNV. So instead of different resistance alleles (i.e., and ), there is only with a differential reaction based on whether it is combined with or , which are tightly linked in repulsion. The new tools and enhanced understanding of this host-virus pathogen interaction will facilitate breeding common beans for resistance to BCMV and BCMNV.