Isoflavones are plant secondary metabolites produced by soybean (Glycine-max-[L.] Merr.) that function as phytoalexins in plants and have positive human health benefits. Breeding for soybeans with high seed isoflavones has attracted considerable attention. Soybean seed isoflavones are quantitatively inherited and may be involved in disease resistance. The objectives of this thesis were to: identify quantitative-trait-loci (QTL) and genes associated with seed isoflavones and study the effects of genotype, environment, and genotype-by-environment interaction (GEI) on isoflavones. A population of 109 recombinant inbred lines was developed from the cross RCAT 1004 x DH 4202 and evaluated in four Ontario locations in 2015 and 2016. Significant genotype, environment, and GEI effects were found. Single marker analyses and interval mapping identified 10 and four QTL associated with isoflavones, respectively. Gene expression analyses revealed the importance of the chalcone synthase 7 and 8 (CHS7 and CHS8) genes on isoflavone biosynthesis. The identified QTL and genes can be used in marker assisted selection.