Eoyukjang is a traditional Korean sauce made of cooked soypaste or meju supplemented with fish and meats at least 1 year of fermentation period. Eoyukjang was recovered according to the traditional method and stored under the ground in a pot without plastic packaging (13G: 13 month fermentation under the ground) or in an incubator wrapped with plastic packaging (6I, 12I, and 18I: 6, 12, and 18 month fermentation, respectively). Distribution of isoflavones and fatty acids were monitored by high performance liquid chromatography (HPLC) and gas chromatography (GC), respectively. Total isoflavones in 13G, 6I, 12I, and 18I were 3.792, 0.387, 0.460, and $0.510{mu}mol/g$, respectively. Samples of 13G had at least 8.24 times higher isoflavone contents than samples from 12I. Aglycones were the major isoflavones in eoyukjang and were found more than 92% in 13G and 39-63% in incubated samples. In fatty acid analysis, the ratios of unsaturated to saturated fatty acids from 13G were higher than those from 6I, 12I, and 18I. Traditional fermentation methods using a pot may allow more migration of air and moisture than samples wrapped with plastic packaging, which caused the difference in the distribution of isoflavones and fatty acids.