Meju, a major ingredient of doenjang which is a popular Korean traditional fermented soyfood, was manufactured by fermenting steamed soybeans in natural environment in which steamed soy was exposed to airborne microorganism, in particular, fungi. Total isoflavone content was reduced from 1,849 mg/kg of cooked soy to 816 mg/kg of meju at the $90^{th}$ day of fermentation. Total glycosides and aglycones of isoflavones in meju were 1,827 and 22 mg/kg at 0 day and changed into 487 and 329 mg/kg at the 90th day of fermentation, respectively. Meanwhile, the ratio of glycosides to aglycones of isoflavones was not changed during aging of doenjang but remained relatively constant with 592 and 644 mg/kg aglycones at the 0 and $160^{th}$ day, respectively. When cooked soy was fermented with Aspergillus oryzae and Aspergillus flavus, isoflavone profiles were significantly different from each other while A. oryzae caused more extensive metabolism of isoflavones than A. flavus.