Charcoal rot is a disease caused by the fungus Macrophomina phaseolina that is common during hot and dry weather. It has long been a problem world-wide including the southern USA, but it is now a threat to the upper Midwest. Management options for reducing the impact of charcoal rot are scarce as fungicide seed treatments are ineffective and crop rotations have little impact. Irrigation is effective in ameliorating the effect of charcoal rot to a degree, but most growers do not have irrigation. Previously, breeding efforts for resistance has been stymied by difficulties in evaluating disease severity across cultivars and environments. Recently, soybean lines with moderate resistance have been identified through field inoculation technique. Identified moderately resistant line was crossed to a susceptible line and the parents, F1s, and F2s of six populations as well as F5 families were phenotyped using colony forming unit. From these crosses, recombinant inbred lines (RILs) have been developed. These RILs are being investigated to understand the genetics of charcoal rot resistance and find QTLs and molecular markers for the resistant genes in the moderately resistant line ‘DT97-4290’. However, additional challenge is faced in understanding the pathogen variation in M.phaseolina. Understanding the degree of variability and characterization of this fungus will enable the understanding of pathogenicity and selection for resistance.