Prevalent on calcareous soils in the United States and abroad, iron deficiency is among the most common and severe nutritional stresses in plants. In soybean commercial plantings, identification and use of iron efficient genotypes has proven to be the best form of managing this soil-related plant stress. Previous studies conducted in soybean identified a significant iron efficiency QTL explaining greater than 70 percent of the phenotypic variation for the trait. In this research we identified candidate genes underlying these QTL through molecular breeding, mapping and transcriptome sequencing. Introgression mapping was performed using two related near-isogenic lines in which a region located on soybean chromosome 3 required for iron efficiency was identified. The region corresponds to the previously reported iron efficiency QTL. The location was further confirmed through QTL mapping conducted in this study. Transcriptome sequencing and qRT-PCR identified, two genes encoding transcription factors within the region that were significantly induced in soybean roots under iron stress. The two induced transcription factors were identified as homologs of the subgroup lb bHLH genes in that are known to regulate the strategy I response in A. thaliana. Re-sequencing of these differentially expressed genes unveiled a significant deletion within a predicted dimerization domain. We hypothesize this deletion disrupts the FIT / bHLH heterodimer that has been shown to induce known iron acquisition genes.