Soybeans (Glycine max (L.) Merr.) genetically modified to express aryloxyalkanoate dioxygenase-12 (AAD-12), an enzyme that confers resistance to the herbicide 2,4-D, can sometimes exhibit a darker seed coat coloration than equivalent unmodified soybeans. The biochemical basis for this coloration was investigated in a non-commercial transgenic event, DAS-411Ø4-7 that exhibited more pronounced AAD-12-associated seed coat coloration than the commercial event, DAS-444Ø6-6. Analysis of color-enriched seed coat fractions from DAS-411Ø4-7 showed that the color was due to localized accumulation of iron-chelating phenolics, particularly the isoflavone genistin, that are associated with seed coat pectic polysaccharide and produce a brown chromophore. The association between genistin, iron, and pectic polysaccharide was characterized using a variety of analytical methods. Darker seeds from commercial soybean event DAS-444Ø6-6 also show higher genistin content localized to the darker colored portions of the seed coat (with no increase in whole seed genistin levels).