More than 30 microorganisms have been recorded as seed-borne on soybeans. The majority have never been known to cause disease as a result of their presence on seeds. For some, such as Peronospora manshurica and soybean mosaic virus, there is concern about transmission of the pathogen to the new crop. For others, such as Phomopsis spp., Cercospora kikuchii and Fusarium spp., the primary concern is the effect on seed quality characteristics of germination and vigor.

Several soil-borne fungi can affect soybean seedling establishment, including Fusarium, Pythium and Rhizoctonia spp. Phytophthora megasperma can cause pre mergence seed rots and damping off as well as disease in older plants.