Charcoal rot incidence in soybean and sunflower in South Africa is increasing. Irrigation as a means to manage charcoal rot is limited as water resources are decreasing and oil seed production is predominantly on dry land. The effect of reduced soil moisture on charcoal rot incidence, severity and colonization of host tissues, as well as subsequent yield loss, was investigated under optimal and sub-optimal conditions for disease development on hosts grown in rotation with Zea mays (maize). Pot experiments were carried out in a greenhouse using a locally planted Glycine max (L.) Merr. (soybean) and Helianthus annuus L. (sunflower) cultivar, which were inoculated with Macrophomina phaseolina (Tassi) Goid. Isolated from sunflower grown in a major oil seed-producing region in South Africa. The disease index, calculated as the product of incidence and severity divided by the total number of observations made per treatment, ((incidence × severity)/(total number of observations made per treatment)), was 20% higher in soybean than in sunflower, even though colonization of sunflower, calculated as the frequency of M. phaseolina isolated from the stem section between the roots and the cotyledon, was 10% more than that of soybean. M. phaseolina was not isolated past the first node of either crop. Yield loss due to charcoal rot amounted to 6.13% in soybean and 12% in sunflower, relative to the uninoculated, reduced soil moisture controls. Microsclerotia were more concentrated in soybean than in sunflower, which indicates that a soybean crop could increase soil inoculum more readily than sunflower. Consideration should therefore be given to the charcoal rot susceptibility of the crop following soybeans. Reduced soil moisture and infection were synergistic to disease incidence and yield loss, but independent of colonization and disease severity. Results showed that an increase in soil moisture cannot prevent initial infection of the host, but can significantly reduce colonization of the stem at maturity.