The purpose of this study was to investigate changes in the amino acid content and physicochemical properties of Cheonggukjang prepared by using various soybean cultivars (Daewon, Deapung, Seadanbeak, and Taekwang) and a functional microorganism (Bacillus subtilis HJ18-9). These soybeans were conventional Cheonggukjang (control) and Cheonggukjang fermented with Bacillus subtilis HJ18-9 (treated). The moisture contents of steamed, control, and treated soybean were 62.45~67.12%, 63.28~67.14%, and 64.50~66.87%; amino-type nitrogen contents were 6.53~24.25 mg%, 27.63~122.09 mg%, and 37.29~133.48 mg%; and ammonia-type nitrogen contents were 26.92~47.95 mg%, 45.45~156.36 mg%, and 28.02~121.13 mg%, respectively. The umami taste associated with several amino acids (aspartic acid and glutamic acid) in Cheonggukjang was lower than that for steamed soybeans, while the bitter taste from amino acids (methionine, valine, isoleucine, leucine, and phenylalanine) was higher than that for steamed soybeans. The result of sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis showed that the molecular weight of steamed soybeans was less than 100 kDa, while control and treated groups showed low molecular weights below 34 kDa, confirming their protein hydrolysis to small molecular weight. These results are information for developing functional fermented soybean paste and diversification using soybean cultivars.