It was observed by electron microscope (transmission electron microscope, Scanning electron microscope) as a study on microstructure of soybean after r-ray irradiation with the intensity of 5KGY, 7KGY, 10KGY and 15KGY, fermented with the named Bacillus subtilis SCF, which newly separated and identified. According to the progress fermentation, changes of soybean microstructure have been increased, especially irradiated soybeans more increased than non-irradiated them. Observation of microstructure by electron microscope showed that each protein body became more. expanded in the dimension and decomposed, spherosome around the protein body in unit area dispersed and dwindled in the numbers of it. As the fermentation on progress, changes of soybean microstructure were suitable on fermentation period of 7KGY soybean, 48-72hrs fermentation.