We developed novel method for producing glucoamylase (GA) from gelatinized rice flour by co-culturing Bacillus amyloliquefaciens NBRC 14141 and Rhizopus cohnii P5. In liquid culture, the acidification of the growth medium due to the growth of R. cohnii prevented the growth of B. amyloliquefaciens; however, the B. amyloliquefaciens protease lysed R. cohnii cells, which decreased the production of GA. This antagonism was repressed by high concentrations of ammonium acetate in the growth medium. However, since low pH or high ammonium acetate concentrations inhibited the initial growth of B. amyloliquefaciens, it needed to be precultured without ammonium acetate. However, preculturing B. amyloliquefaciens for 48 h led to overproduction of protease, which inhibited the growth of R. cohnii. As a result, the maximum GA activity (740 U/ml) was obtained when B. amyloliquefaciens was precultured for 24 h followed by inoculation with R. cohnii in the presence of 3.84% (w/v) of ammonium acetate. These results indicated that GA can be produced at high levels from gelatinized rice flour by using a submerged co-culture system.