Poor grain quality resulting from delayed harvest can cause major economic losses in the U.S. soybean production system. Phomopsis seed decay, caused by Phomopis longicolla (PL), can contribute to reduced quality in harvested grain. The objective of this research was to determine differences in grain damage between soybean entries under environmental conditions conducive to effecting harvested grain quality and identify contributing organisms. Two rainout shelters were used for experiments. Each shelter contained 21 entries planted as single row plots on 76.2 cm centers and 3.6 m in length, replicated three times. Both shelters were inoculated with a PL spore suspension at R5.5. An application of 118.3 ml/ha of trifloxystrobin + prothioconazole was applied at R7 to plots in shelter 2, but not shelter 1. Shelters were overhead irrigated for 200 h. Plots were hand-harvested at R8. Symptoms associated with Phomopsis seed decay were observed on grain. Hundred kernel weights and germination percentages were determined from grain post-harvest. Significant differences were observed in the non-fungicide shelter with a 78% difference in weight between Progeny 4211 and 11030-541-210 and an 81% difference in damage between 11030-541-210 and DB06X06-093. No significant differences in plot weight, hundred kernel weight or grain damage were observed in the fungicide-treated shelter. The internal spacer region (ITS) was used to determine the fungi present on harvested grain.