Anthocyanin pigments in black soybean seed coat have been known as including biological activities, which are antitumor, antioxdant and antivirus. Also in soybean, isoflavone have been reported as health-promoting benefits, which are antiestrogen, antioxidant, antitumoral activities and preventing cardiovascular diseases and osteoporosis. The consumption of soybean increased in Korea because of the importance of its functional characteristics of the anthocyanin and isoflavone. Therefore, this experiment was conducted to investigate the variation of anthocyanin, and isoflavone contents in Korean domestic black soybean cultivars grown at different latitudinal locations, Suwon (37°16'N) and Milyang (35°30'N). D3G, C3G, and total anthocyanins in Geomjeongkong # 3, C3G, and total anthocyanins in Ilpumgeomjeongkong grown at higher latitudinal Suwon were higher compared to lower latitudinal Milyang. Daidzein, glycitein, genistein, and total isoflavone contents in Gemjeongkong # 4 were highest among the seven cultivars. Daidzein contents in Gemjeongkong # 3, Milyang # 112, and Milyang # 113 grown at higher latitudinal Suwon were higher compared to lower latitudinal Milyang. Glycitein contents in Gemjeongkong # 3, and # 4 grown at higher latitudinal Suwon were higher Milyang while that in Milyang # 113 grown at lower latitudinal Milyang was higher compared to higher latitudinal Suwon. Genistein contents in most black soybean cultivars except Milyang # 113, and total isoflavone contents in Gemjeongkong # 4 and Cheongjakong grown at lower latitudinal Milyang were higher compared to higher latitudinal Suwon. The variations of anthocyanin except Pt3G and isoflavone contents seemed to be affected by environmental conditions like different latitude than the genotype because they showed the significant interaction between cultivars and locations.