Infection of soybean by Bean pod mottle virus (BPMV) or Soybean mosaic virus (SMV) has been reported to increase susceptibility to seed infection by Phomopsis spp., but the mechanism is unclear. Effects of virus infection on susceptibility to Phomopsis longicolla were studied in greenhouse experiments. Three soybean cultivars were inoculated with BPMV at growth stage V2 to V3, and with P. longicolla at R3, R5, or R7. Inoculation with BPMV did not increase the incidence of stem infection by P. longicolla, but it increased susceptibility to seed infection of cultivars Spansoy 201 at R5, and Pioneer brand 92M02 at R3, R5, and R7. A delay in maturity was observed only in 92M02. Thus, BPMV predisposed soybean plants to seed infection by P. longicolla, but this predisposition was not due solely to prolonging maturation. In separate experiments, two soybean cultivars were inoculated with SMV (V2 to V3) and P. longicolla (R3 and R5). Inoculation with SMV did not increase the incidence of stem or seed infection by P. longicolla. The SMV–Phomopsis spp. relationship may be cultivar and strain dependent. Results suggest that the risk of soybean seed infection by P. longicolla may be higher when BPMV vector populations are high and BPMV infection is widespread.