Flavonoids are a group of secondary metabolites found in many higher plants. The multiple roles of their flavone subclass include protection against UV damage, regulation of auxin transport, and modulation of flower color. In soybean (Glycine max), flavone synthase II (FNS II) is the key enzyme responsible for flavone biosynthesis. Two FNS II genes from soybean cultivar Hefeng 47 were cloned according to basic local alignment search tool (BLAST) contexts using flavone synthase sequences reported in other species. These were named GmFNSII-1 and GmFNSII-2. Sequence alignments showed that the cDNA of GmFNSII-1 was identical to that of CYP93B16, whereas GmFNSII-2 was clearly distinct. Functional assays in yeast (Schizosaccharomyces pombe) suggested that these two enzymes could convert (2S)-naringenin into apigenin. The two GmFNSII genes had similar tissue-specific expression patterns, but GmFNSII-2 was significantly expressed in the roots after treatment with 0.4 M glucose. This demonstrates that the gene plays an important role in the response to defense signals in soybean. RNA interference-mediated suppression of those GmFNSII genes effectively regulated flavone and isoflavone production in hairy roots that arose from soybean cotyledons transformed with Agrobacterium rhizogenes (ATCC15834). Our study also highlights some of the challenges associated with metabolic engineering of plant natural products.