To establish the optimal manufacturing conditions of soybean koji, soybean Koji prepared with Aspergillus oryzae 6-M-1 and Bacillus subtilis 3-B-1 isolated from traditional Korean meju. During 7 days of making Koji, the amount of amino-type nitrogen was getting more increase. The amount of amino-type nitrogen of Koji prepared with A. oryzae 6-M-1 was 686.16 mg% (w/w), that of Koji with B. subtilis 3-B-1 was 643.46 mg% (w/w) at seventh day of making Koji. The α-amylase activity of Koji prepared with A. oryzae 6-M-1 was 1472.54 unit/g, that of Koji with B. subtilis 3-B-1 was 791.00 units/g on the seventh day of the making. The acidic protease activity of Koji prepared with A. oryzae 6-M-1 was 309.00 unit/g, that of Koji with B. subtilis 3-B-1 was 135.88 unit/g at 7th day of making. The amount of amino-type nitrogen and enzyme activities of soybean Koji prepared with A. oryzae 6-M-1 and B. subtilis 3-B-1 were produced more than those of wheat flour Koji made in factory. Sensory evaluation on a commercial doenjang and doenjangs prepared with A. oryzae 6-M-1 and B. subtilis 3-B-1 was not significantly different at p<0.05.