Proanthocyanidins (PAs) as the end products of flavonoid biosynthetic pathway mainly accumulate in seed coat but their biological function is largely unknown. We studied the anti-oxidation ability in seed coat and germination changes under externally applied oxidative stresses in PAs-deficient mutants of Arabidopsis. Germination of PAs-deficient mutant seeds was faster than that of wild-type under low or no oxidative stress, suggesting a PAs-induced inhibition of germination. When the applied oxidative stress was high, germination of PAs-deficient mutants was lower than that of wild-type, suggesting a loss of PAs-related anti-oxidation ability in the mutants. Using ABA signaling mutants, our studies demonstrated that both ABA signaling pathway and PAs were important for the response to serve oxidative stress during seed germination. However, the discrepancy of the response between abi mutants and PAs mutants to oxidative stress suggests that ABA signaling pathway may not play a major role in PAs' action in alleviating oxidative stress. Under low or no oxidative stress, germination was mainly determined by the ABA content in seed and the PAs-deficient mutant seeds germinated faster due to their lower ABA content than wild-type. However, oxidative injury inhibited germination when PAs-deficient seeds germinated under high oxidative stress. Wild-type exhibited higher germination under the high oxidative stress due to the PAs' anti-oxidation ability. Oxidative stress applied externally led to changes in endogenous PAs contents that coincided with the expression changes of PAs biogenesis genes. PAs modulated the activities of some key enzymes that controlled the levels of reactive oxygen species and the anti-oxidation capacity during the seed germination. This work suggests that PAs contribute to the adaptive mechanism that helps germination under environmental stresses by playing dual roles in both germination control and anti-oxidation reaction.