Soybean (Glycine max L.Merr.) is the world's foremost source of edible plant oil and proteins,meantime,the biologically active secondary metabolites such as saponins and isoflavones are benefit to human health.The objective of this study was to identify quantitative trait loci (QTL) and epistatic interactions associated with isoflavone,protein,and oil contents in soybean seeds.An F13 recombinant inbred line (RIL) comprising 474 lines was derived from a cross between Jindou 23 and Huibuzhi cultivars.SSR technique was employed for mapping of the QTLs.The QTLs for isoflavone,protein,and oil contents were analyzed and 23 QTLs were detected based on the constructed linkage map.Six QTLs for isoflavone content were localized in linkage groups J,N,D2,and G,eleven QTLs for oil content were localized in the linkage groups A1,A2,B2,C2,and D2,and six QTLs for protein content were localized in linkage groups B2,C2,G,and H1.The correlative analysis demonstrated that the isoflavone content had significant correlation with protein content,while significantly negative correlations was existed between oil and protein content,and significantly positive correlations was existed between protein and oil content.All these findings have laid an important basis for the marker assisted breeding in soybean.The phenotypic correlations of quantitative traits may be resulted from the correlation of the QTL controlling those traits.