Abstract Bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV) have a damaging impact on global common bean ( Phaseolus vulgaris L.) cultivation, causing potential yield losses of over 80%. The primary strategy for controlling these viruses is through host plant resistance. This research aimed to identify and validate structural variations for the bc‐u d gene as revealed by long‐read sequencing, develop an efficient DNA marker to assist selection of bc‐u d in snap and dry beans, and examine the interactions between the bc‐u d allele and other BCMV resistance genes. A gene (Phvul.005G125100) model on chromosome Pv05, encoding a vacuolar protein‐sorting 4 (Vps4) AAA+ ATPase endosomal sorting complexes required for transport (ESCRT) protein, was identified as the best candidate gene for bc‐u d . An 84‐bp repetitive insertion variant within the gene, exhibited 100% co‐segregation with the bc‐u d resistance allele across 264 common bean accessions. The 84‐bp repetitive insertion was labeled with an indel marker IND_05_36225873 which was useful for tracking the bc‐u d allele across diverse germplasm. A different single nucleotide polymorphism variant within the same candidate gene was associated with the bc‐4 gene. Segregation in F 2 populations confirmed bc‐u d and bc‐4 were alleles, so bc‐4 was renamed bc‐u r to fit gene nomenclature guidelines. The interactions of bc‐u d and bc‐u r with other resistance genes, such as bc‐1 (receptor‐like kinase on Pv03) and bc‐2 (Vps4 AAA+ ATPase ESCRT protein on Pv11), validated gene combinations in the differential “host groups” effective against specific BCMV/BCMNV “pathogroups.” These findings increase our understanding of the Bc‐u locus, and enhance our ability to develop more resilient bean varieties through marker‐assisted selection, reducing the impact of BCMV and BCMNV.