Soil flooding is a seasonal factor that negatively affects plant performance and crop yields. In order to investigate the effects of spermidine (Spd) and spermine (Spm) on the waterlogging stress, it was checked that the content of relative water content (RWC), proline, chlorophyll and malondialdehyde (MDA), net photosynthesis, the rate of hydrogen peroxide (H(2)O(2)) and superoxide radicals (O(2)(-)) generation and the antioxidant enzyme activities of superoxide dismutase (SOD) (EC 1.15.1.1), catalase (CAT) (EC 1.11.1.6), ascorbate peroxidase (APX) (EC 1.11.1.11) and glutathione reductase (GR) (EC 1.6.4.2) in Welsh onion (Allium fistulosum L) plants. Pretreatment with 2 mM of Spd and Spm effectively maintained the balance of water content in plant leaves and roots under flooding stress. In addition, the data indicate that the protective role of proline should be considered minimal, as its accumulation was found to be inversely correlated with tolerance to stress; it also significantly retarded the loss of chlorophyll, enhanced photosynthesis, decreased the rate of O(2)(-) generation and H(2)O(2) content, and prevented flooding-induced lipid peroxidation. Spd and Spm helped to maintain antioxidant enzyme activities under flooding; however, APX activity was found to increase slightly in response to Spm. The antioxidant system, an important component of the water-stress-protective mechanism, can be changed by PAs, which are able to moderate the radical scavenging system and to lessen in this way the oxidative stress. The results suggest that pretreatment with Spd and Spm prevents oxidative damage, and the protective effect of Spd was found to be greater than that of Spm.