Isoflavones are secondary metabolites present in seeds of soybean [ Glycine max (L.) Merr.] which have been recognized their benefit to human health. In this study, QTL mapping for soybean isoflavone gylcones including daidzin, glycitin and genistin and total isoflavones content was performed in population of 178 F2:6 recombinant inbred lines (RILs) which was generated from cross between varieties Jinong17 and Jinong18. A genetic linkage map covering 1248 cM was constructed using the simple sequence repeat (SSR) molecular markers. The results revealed 22 isoflavone- related QTLs, 5 for daidzin, 7 for genistin, 6 for glycitin, and 4 for total isoflavone content. Seven of these represent new QTLs. Twenty candidate genes were identified, including eight laccases with presumed role in lignin biosynthesis, and the transcriptional regulator BANYULS and all three components of the MYB-bHLH-WD40 (MBW) complex that regulate its expression. These findings suggest that alterations in lignin and proanthocyanidin metabolism influence isoflavone accumulation in seeds. These leads might be helpful in the efforts to breed new soybean varieties with improved isoflavone composition and content.