Technical Abstract: Soybean (Glycine max [L] Merr.) seed isoflavones have long been considered a desirable trait to target in selection programs for their involvement on fitness for humans and the plant per se. However, attempts to modify seed isoflavone content have not always produced the expected results because their genetic basis is polygenic and complex. Undoubtedly, the extreme variability that seed isoflavones display over environments has obscured our understanding of the genetics involved. In this study, a mapping population of RILs with three replicates was analyzed in two locations and in two years. We found a total of thirty five main-effect genomic regions controlling genistein, daidzein, glycitein and total isoflavones accumulation in seeds. The use of distinct environments permitted detection of a great number of environment-modulated and minor-effect QTL. Our findings suggest that isoflavone seed concentration is controlled by a complex network of multiple minor-effect loci interconnected by a dense epistatic map of interactions. We hypothesize that the magnitude and significance of the main and epistatic effects of the nodes in the network will vary depending on the genetic background and environmental conditions. In an attempt to unravel the genetic architecture underlying the traits studied, we searched on a genome-wide scale for genomic regions homologous to the most important identified isoflavone biosynthetic genes. We identified putative candidate genes for several of the main-effect and epistatic QTL and for QTL reported by other groups.