This study was attempted to develop technique of masking the pungent odor of chonggugjang using two-stage fermentation method with mixed pure cultures. Cooked soybeans were fermented with Lactobacilli or Aspergillus oryzae at 38℃ far 36 hrs, and then re-fermented with Bacillus subtilis for 12 hrs. The volatile compounds of chonggugjang were obtained with a SDE(Simultaneous steam Distillation and solvent Extraction) system and the extracts were identified by GC and GC-MS. The experimental results revealed the presence of 35 volatile compounds in control chonggugjang(only Bacillus subtilis inoculation). Among them, the major volatile compounds were 2,5-dimethyl pyrazine, 2,3,5-trimethyl pyrazine and 2-methyl pyrazine. Twenty-nine kinds of volatile compounds were in chonggugjang prepared by two-stage fermentation method with Lactobacilli and Bacillus subtilis(II), and major volatile compounds were identified to be 2,3,5-trimethyl pyrazine and 2,5-dimethyl pyrazine. In chonggugjang(Asp. oryzae and then Bacillus subtilis inoculation(III)), the contents of hexadecanoic acid and 2-methyl pyrazine were particularly high and the main components of chonggugjang fermented with rice straw(IV) were 2,5-dimethyl pyrazine, 2,3,5-trimethyl pyrazine etc. In conclusion, the flavor compounds such as 2,5-dimethyl pyrazine, 2,3,5-trimethyl pyrazine and 2-methyl pyrazine were increased by the inoculation of Lactobacilli or Asp. oryzae, where as unpleasant odor components-butyric acid and valeric acid were decreased. Compared with volatile compounds of chonggugjang made from different soybean cultivars, the flavor compounds (2-methyl pyrazine·2,5-dimethyl pyrazine·2,6-dimethyl pyrazine·2,3-dimethyl pyrazine·2-acetyl pyrazine·2,3,5-trimethyl pyrazine·2-ethyl-3,5-dimethyl pyrazine) of chonggugjang prepared with Sinpaldalkong were high.