Plant-derived folates (vitamin B9) are essential components of the human diet. Putative folate biosynthesis genes were identified in the syntenic Phaseolus vulgaris L. and Glycine max (L.) Merr. genomes with the latter having undergone whole genome duplication (WGD). For most of the folate synthesis enzymes, two and four genes were discovered in P. vulgaris and G. max, respectively. Analysis of publicly available RNAseq data in both species demonstrated that one copy of each duplicated gene was ≥2-fold more highly expressed than the other. Expression of genes neighboring the folate structural genes were examined in order to determine whether or not the duplicated regions exhibited biased differential expression (genome dominance). Additionally, P. vulgaris and G. max synteny was characterized and gene retention following the WGD was examined. A subgenome bias in gene retention is known as biased fractionation. Neither genome dominance nor biased fractionation was observed in the G. max genome. The present work provides a phylogenetic and genomic analysis of this important biochemical pathway in two staple crops. The development of high-folate cultivars is necessary in order to reduce the prevalence of folate deficiency which leads to numerous adverse human health conditions. A diverse population of 100 P. vulgaris accessions, including several market classes, was grown in two years in Ontario, Canada. Total folate content across the population varied from 113 to 222 µg per 100 g of seeds. The accessions were genotyped for 5361 single nucleotide polymorphism markers, and a genome-wide association study was conducted for seed folate content. Six quantitative trait loci (QTL) were identified on chromosomes 4, 6, 8, and 11. Candidate genes on this QTL included an S-adenosylmethionine-dependent methyltransferase, a uridine diphosphate-dependent glucosyltransferase, an HXXXD-type acyltransferase, and a secretory protein 14 (SEC14)-like gene. This work reports the largest survey of genetic diversity for seed folate content in P. vulgaris and identified several genotypes, including SCN4, Bat 93, OAC Redstar, and Pompadour 1014, that would be useful for breeding beans with higher than average folate levels.