Soybean isoflavones include daidzein, genistein and glycitein with their glycosides, and their malonated derivatives are the main polyphenolic compounds that are helpful for human health. Our research objective was to investigate the differentitation of soybean isoflavones contents of breeding populations between yellow and black soybean. Isoflavones contents in soybean are a wide range from 500 to 7000 ㎍/g. In this study, we used Ilmi (Isoflavones content, 3.612 ㎍/g) as male parent and 04GAYT-4 (Isoflavones content, 1,648 ㎍/g) as female parent. From these varieties, we obtained 94 breeding lines (yellow, 48 lines; black, 25 lines; brown, 21 lines) which have isoflavones content range from 1000 to 6000 ㎍/g. Highest isflavone contents of three different breeding lines was yellow seed coated lines (average isoflavone content, yellow 3,046 ㎍/g, brown 2,935 ㎍/g, black 2,813 ㎍/g).