In this report we compared the total contents and the distribution of isoflavones in six soybeans, including 1 imported genetically modified (GM) soybean and 5 Taiwanese nongenetic modified soybeans, Koushing 10, Tainan 1, Tainan 4, Tainan 5 black, and commercial black. After the soybeans were soaked for 0, 4, 8, 12 and 16 hr in the solutions with different pH values (pH 3, 7 and 9), the contents of the isoflavones in the different 6 soybeans were measured. Nine isoflavones, including daidzin, genistin, and glycitin with a glucoside; acetyl-daidzin, acetyl-genistin, and acetyl-glycitin with acetylglucoside; and daidzein, genistein, and glycitein aglycones, were measured by HPLC. The total content of the isoflavones in Soybean Kaohsiung 10 was the highest at approximately 346 mg/100g. Soybean Tainan 5 black is the one with the lowest content of isoflavones. The isoflavones were present predominantly in forms with glucoside. After soaked in the water for different lengths of time, there was no significant loss of total isoflavones. In GM soybean, Koushing 10, and Tainan 5 black, the contents of aglycons, diadzein and genistein aglycones increased significantly after the soybeans were soaked in the water for 4 hr, compared with the ones in unsoaked soybeans (P < 0.05). In GM soybean, Koushing 10, and Tainan 5 black, the total contents of isoflavones in the soybeans soaked after 8 hr in pH 9 solutions were obviously lower than the ones in pH 3 and pH 7. The level of daidein and genistein from Kaohsiung 10 soaking in pH 3 was higher than pH 7 and pH 9. The contents of deidzein and genistein in Koushing 10 soaked in pH 3 solution was the highest, while the contents of deidzein and genistein in Tainan 5 black soybean soaked in pH 9 solution was the lowest.