This study assessed the altitudinal variations in the anthocyanin and isoflavone contents of six black seed coated soybean [Glycine max (L.) Merrill] cultivars. The black soybean cultivars Heugcheong, Seonheuk, Geomjeong 1, Geomjeong 2, Cheongja 2, and Cheongja 3 were planted at Milyang (12 m above mean sea level - low altitude) and Muju (600 m - high altitude), Korea on 10 June 2005 and 2006. The total anthocyanin and isoflavone contents and individual components were investigated by reverse-phase high performance liquid chromatography (HPLC). All black soybean cultivars cultivated in high altitude possessed significantly higher total anthocyanin (p < 0.01) and isoflavone (p < 0.01) contents than those grown in low altitude. For anthocyanin composition, cyanidin-3-O-glucoside, cyanidin-3-O-galactoside, and peonidin-3-O-glucoside contents were significantly higher while delphinidin-3-O-glucoside contents was significantly lower at high altitude. The composition of individual isoflavones, 6"-O-malonyldaidzin, and 6"-O-malonylgenistin contents significantly increased at high altitude.