The bacterial diversity in Korean soybean-fermented foods was investigated using a PCR-based approach. 16S rRNA sequences were amplified and cloned from two different soybean-fermented foods such as doenjang (soybean paste), and ganjang (soybean sauce). Staphylococcus equorum (60.6%), Tetragenococcus halophila (21.2%), Leuconostoc mesenteroides (9.1%), Lactobacillus sakei (6.1%), and Bacillus subtilis (3.0%) were detected among clones isolated from soybean paste samples and Halanaerobium sp. (37.5%), Halanaerobium fermentans (37.5%), T. halophila (12.5%), Staphylococcus sp. (6.3%), S. equorum (3.1%), and B. subtilis (3.1%) were detected among clones isolated from soybean sauce. Our approach revealed different bacterial distributions and diversity from those previously obtained using culture-dependent methods.