Thirty five genera of internally seedborne fungi were isolated from soya bean seed produced at Isabela, Puerto Rico. When seeds were inoculated with these fungi and plated on potato-dextrose agar (PDA), 19 genera significantly reduced soya bean seed germination in vitro. When inoculated seeds were planted in sterile sand, the percentage seed germination and seedling emergence were greater than in vitro germination (PDA). Fourteen genera significantly reduced seedling emergence in sand. Only six genera significantly reduced seedling emergence in the field. Of the 35 genera tested, Phomopsis sp., Sclerotium rolfsii, Lasiodiplodia theobromae, Colletotrichum dematium, Macrophomina phaseolina and Cephalosporium gregatum were the most pathogenic to soya bean seed under all test conditions. The majority of the fungi tested in this study appeared to be saprophytes, which have no or very little effect on soya bean seed germination in vitro or emergence in the field.