In this study, the concentrations of isoflavones, anthocyanins and total phenol content (TPC) in 19 soybean mutant lines changed seed coat color from yellow to black or brown were determined. Among 19 soybean mutant lines, 5 soybean mutant lines with black pigment were detected 3 anthocyanins (delphinidin-3-O-β-D-glucoside, D3G; cyaniding 3-O-β -D-glucoside, C3G; petunidin 3-O-β-D-glucoside, Pt3G). The highest concentration of anthocyanins among 5 soybean mutant lines was D-16 (1280.0 ± 19.4 mg/100g seed coat) derived from cv. Danbaek. Although isoflavone contents of all soybean mutant lines showed lower levels compared to original cultivars, glycitein was detected only 5 soybean mutant lines (DP-37-2, DP-38, DP-39, DP-40, and DP-41 derived from cv. Daepung). In TPC of 19 soybean mutant lines, DP-10 was increase levels compared to original cultivar, while DP-37-2, DP-40, and DP-41 were decrease levels of TPC. Using reduction of DPPH, we measured the free radical scavenging activity (FRSA) among 19 soybean mutant lines. Five black and 4 brown soybean mutants showed significant increase in FRSA. On the basis of these results, it was concluded that gamma irradiation may change the isoflavone, anthocyanin, and total phenol contents of soybean. These mutant lines using in this study can be useful for the breeding of soybean varieties altering the nutritional values.