<p>  </p> <p><em>Sclerotinia sclerotiorum </em>is a soilborne pathogen of soybean that causes Sclerotinia stem rot, alternatively called white mold. Sclerotinia stem rot can cause significant yield losses under cool and wet environmental conditions. Two biofungicides, <em>Coniothyrium minitans </em>and <em>Bacillus amyloliquefaciens, </em>are currently available and labeled to limit or suppress <em>S. sclerotiorum</em> in soybean. These biofungicides can be applied in place of synthetic foliar fungicides to provide an alternative mode of action for the control of Sclerotinia stem rot. However, limited information is available regarding the efficacy of <em>C. minitans </em>and <em>B. amyloliquefaciens </em>as biocontrol agents of <em>S. sclerotiorum </em>in soybean and the sensitivity of the biofungicides biological activity on <em>S. sclerotiorum </em>to pesticides commonly used in soybean production systems. This research aims to provide management recommendations for <em>S. sclerotiorum </em>in soybean using <em>C. minitans </em>and <em>B. amyloliquefaciens </em>and to develop guidelines for how to incorporate the biofungicides into an established soybean pest management program. To assess the effectiveness of <em>C. minitans </em>and <em>B. amyloliquefaciens </em>as biocontrol agents of <em>S. sclerotiorum </em>dual culture, amended media, and soil plate assays were conducted along with experiments in the growth chamber and field. The presence of a distinct inhibition zone surrounding the <em>B. amyloliquefaciens </em>colony in the dual culture assay and the absence of mycelial growth on the media plates amended with <em>B. amyloliquefaciens </em>confirmed that the bacteria can control the mycelial growth of <em>S. sclerotiorum </em>through antibiosis. The absence of an inhibition zone surrounding the <em>C. minitans </em>isolate in the dual culture assay along with the degradation of sclerotia following treatment with <em>C. minitans </em>in the soil plate assay indicates an inability to limit the mycelial growth of <em>S. sclerotiorum </em>and confirms that the primary mode of action is mycoparasitism. In the growth chamber, <em>B. amyloliquefaciens</em> at 14.03 L/ha applied using the dip method significantly reduced Sclerotinia stem rot lesion length when compared to the non-treated control and resulted in the lowest lesion area under the disease progress curve (lAUDPC). When <em>B. amyloliquefaciens </em>and <em>C. minitans </em>were applied in the field, no differences were observed between treatments for soybean moisture, test weight, or yield. To evaluate the sensitivity of <em>B. amyloliquefaciens </em>and <em>C. minitans</em> biological activity on <em>S. sclerotiorum </em>to pesticides commonly used in soybean production systems a poison plate assay as well as soil plate, growth chamber, and field experiments were conducted. In the poison plate assay <em>C. minitans </em>was most sensitive to the preemergence herbicide flumioxazin and the synthetic fungicides boscalid and fluazinam, while <em>B. amyloliquefaciens </em>was sensitive only to the synthetic fungicide fluazinam. In the soil plate assay the mycoparasitic activity of <em>C. minitans </em>on sclerotia of <em>S. sclerotiorum </em>was sensitive to flumioxazin, metribuzin, glyphosate, picoxystrobin, and boscalid. In the controlled environment experiments, none of the pesticides tested decreased the efficacy of <em>B. amyloliquefaciens</em>. There were no significant interactions between <em>C. minitans </em>and <em>B. amyloliquefaciens </em>with preemergence herbicides, postemergence herbicides, and synthetic fungicides for soybean moisture, test weight, and yield. This research demonstrates that <em>B. amyloliquefaciens </em>and <em>C. minitans </em>are effective biocontrol agents of <em>S. sclerotiorum </em>in soybean. However, antagonistic relationships exist between the biofungicides and certain preemergence, postemergence, and synthetic fungicides used in soybean production systems.</p>