Abstract: As natural antioxidants, flavonoids, containing polyphenolic hydroxyls and conjugated electronic structures, can inhibit chain oxidation reaction by scavenging radicals. The antioxidation active sites of flavonoids and the stabilities of product radicals are the basically factors on affecting their antioxidant reactivities. This work compares the dynamics of radicals formed from photooxidation on anionic daidzein and genistein, respectively, as revealed by the use of time-resolved spectroscopies combined with quantum chemical analyses. It is found that direct photooxidation of mono- and di-anionic daidzein both formed an intermediate radical which transformed into a relatively more stable radical via intramolecular electron trasfer. Photooxidation of anionic genistein, an isoflavone with one more 5-hydroxyl than daidzein, including mono-, di- and tri-anions, results in the formation of a stable radical with electronic spin density delocalizing on the whole molecular backbone. The antioxidant reactivity of 4’-hydroxyl for mono-anion is enhanced by the presence of 5-hydroxyl, which is ascribed to the key structural factor for the higher antioxidant activity of genistein than daidzein in physiological condition.