AbstractIn this study, the flavonoid and isoflavone contents in four checks with seed coat colour altered from yellow to black were determined, and their antioxidant activity was measured. Three anthocyanins (delphinidin‐3‐O‐β‐D‐glucoside, D3G; cyanidin‐3‐O‐β‐D‐glucoside, C3G; and petunidin‐3‐O‐β‐D‐glucoside, Pt3G) were detected in the four checks, while their controls (cvs. ‘Danbaek’ and ‘Daepung’) were not found. Among them, D‐16 derived from cv. ‘Danbaek’ showed the highest anthocyanin contents. The isoflavone contents of all checks showed lower levels compared to their controls. Among six isoflavones, glycitein was only detected inDP‐39. To analyse the radical scavenging activities among the four checks, we conductedDPPH,FRAPandUWLAassays. Significant differences in antioxidant activities were obtainable in the four checks, which contained significant differences in levels of anthocyanins and isoflavones. Based on these results, gamma irradiation may change the isoflavone and anthocyanin contents of soybean. Our four checks selected in this study may be useful for breeding soybean varieties to alter their nutritional values.