Our research objective was to increase isoflavone content in the germinated soybean seeds of four different varieties (Pungsannamulkong, Cheongjakong, Aga4, and Aga3) by optimizing light treatments (dark, greenhouse, fluorescent, incandescent, and ultraviolet lamps). The results demonstrated that the highest isoflavone content was produced from the Aga3 variety, which was developed by an interspecific cross between Eunhakong (Glycine max) and KLG10084 (G. soja) at the Plant Genetic Laboratory, Kyunpook National University. Aga3 is known to have one of the highest isoflavone content in the world at present. Our results recommend exposure of 7-day-old Aga3 sprouts to a combined light treatment of greenhouse lamps (12 h per day) and ultraviolet light (40 min per day) for maximum isoflavone production. Aga3 produced high levels of isoflavone because, in part, it contained very high isoflavone levels within the seed as compared with the other varieties. Under stress conditions, Aga3 could produce over 1.90 times more isoflavone than its seed content and 1.53 times more isoflavone than when grown under dark conditions.