Infection of soybean [Glycine max (L.) Merr.] plants with Soybean mosaic virus (SMV) has been reported to enhance Phomopsis spp. seed infection, which reduces seed quality. The objective of this study was to determine the influence of SMV on Phomopsis spp. seed infection and seed germination and vigor. During 1995 to 1997, plants of two SMV‐susceptible cultivars (Clark and Williams) and their SMV‐resistant isolines (L78‐434 and L78‐379, resistant to SMV strains G1‐G6) were mechanically inoculated with SMV (G2 strain) at growth stages V4, V8 or R2, and Phomopsis spp. inocula were applied to all plants. Seeds harvested from SMV‐resistant isolines were consistently SMV free, whereas seeds from SMV‐inoculated susceptible cultivars accumulated SMV in seedcoats. Although environmental conditions were favorable, the incidence of Phomopsis spp. seed infection was consistently less than 12% in SMV‐resistant plants, and up to 14‐times greater in SMV‐inoculated susceptible plants, with primary infection occurring after seeds reached physiological maturity (at or after yellow pod stage). Seeds from SMV‐resistant isolines had high average standard germination (88%) and higher vigor (67% accelerated aging; 7 mS m−1 g−1 conductivity), whereas seeds from SMV‐inoculated susceptible cultivars had low standard germination (48%), low vigor (30% accelerated aging; 13 mS m−1 g−1 conductivity). Thus, infection by SMV at or before growth stage R2 increased the susceptibility of soybean seed to Phomopsis spp. infection, and resulted in poor seed quality and low vigor.