The objectives of this study were to identify the antioxidants in acid hydrolysates of six of Taiwan’s indigenous purple-leaved vegetables (IPLV), including purple-leaved sweet potato (Ipomoea batatas L. Lamark), purple-leaved gynura line 1 (Gynura bicolor D.C.), purple-leaved gynura line 2 (Gynura bicolor D.C.), purple-leaved perilla line 1 (Perilla frutescents L. Britton), bicolored-leaved perilla line 2 (Perilla frutescens L. Britton), and heartleaf houttuynia (Houttuynia cordata Thumb.). Their antioxidant activity and ability to protect DNA from oxidative damage was also evaluated. The antioxidants identified included flavonoids, anthocyanidins and flavonols. Both purple-leaved perilla line 1 and bicolored-leaved perilla line 2 were found to be abundant in cynidin, malvidin, and myricetin. Moreover, purple-leaved sweet potato and heartleaf houttuynia were found to be abundant in quercetin. Purple-leaved sweet potato and purple-leaved perilla line 1 contained significantly higher inhibition percentages of conjugated diene formation than other vegetables. Purple-leaved sweet potato, heartleaf houttuynia, purple-leaved perilla line 1, and bicolored-leaved perilla line 2 had better inhibition percentages of tail DNA% and tail moment in the study. In conclusion, the abovementioned four indigenous purple-leaved vegetables abounded in antioxidants had strong antioxidant activity for protecting DNA in lymphocytes from oxidative damages.