Dry common bean (Phaseolus vulgaris L.) is a food crop that is an important source of dietary proteins and carbohydrates. Marsh spot is a physiological disorder that diminishes seed quality in beans. Prior research suggested that this disease is likely caused by manganese (Mn) deficiency during seed development and that marsh spot resistance is controlled by at least four genes. In this study, genetic mapping was performed to identify quantitative trait loci (QTL) and the potential candidate genes associated with marsh spot resistance. All 138 recombinant inbred lines from a bi-parental population were sequenced using a genotyping by sequencing approach. A total of 52,676 single nucleotide polymorphism (SNP) markers were identified and filtered to generate a high-quality set of 2,066 SNPs for QTL mapping. A genetic map based of 1,273 SNP markers distributed on 11 chromosomes and covering 1,599 cM was constructed. A total of 16 QTL were identified using additive effect models, and an additional two epistatic QTL interacting with two of the 16 QTL were identified using an epistasis model. Genome-wide scans of the candidate genes identified 13 metal transport related candidate genes co-locating within eight QTL regions. In particular, two QTL (QTL.3.1 and QTL.3.2) with the highest R2 values (21.8% and 24.5%, respectively) harbored several metal transport genes Phvul.003G086300, Phvul.003G092500, Phvul.003G104900, Phvul.003G099700, and Phvul.003G108900 in a large genomic region of 16.8 – 27.5 Mb on chromosome 3. These results advance the current understanding of the genetic mechanisms of marsh spot resistance in cranberry common bean, and provide new genomic resources for use in genomics-assisted breeding and for candidate gene isolation and functional characterization.