Aerobic rice offers an attractive alternative approach over transplanting system as it consumes less water with low labour expenses. Flag leaf of six rice cultivars, viz. PR 120, PR 115, PR 116, Feng Ai Zan, PAU 201 and Punjab Mehak 1 was analysed for antioxidant defence mechanism and polyamine catabolism under the aerobic and the transplanting conditions. Ascorbate peroxidase (APX), guaiacol peroxidase (GPX), catalase (CAT), superoxide dismutase (SOD), diamine oxidase (DAO) and polyamine oxidase (PAO) activities increased gradually from tillering to anthesis stage and then declined towards maturity stage under both planting conditions. Apparently, contents of ascorbic acid, α-tocopherol, proline and polyamines (PAs) also revealed similar trend. The aerobic condition elevated activities of PAO, SOD as well as contents of PAs, lipid peroxide and H2O2 whereas the transplanting condition had higher levels of APX, GPX, CAT and total antioxidant activities and contents of ascorbate, α-tocopherol and proline. Cultivars Feng Ai Zan, PR 115 and PR 120 exhibited superior tolerance over other cultivars by accumulating higher contents of PAs with increasing levels of PAO and SOD activities under the aerobic condition. However, under the transplanting condition PR 116 and PAU 201 showed higher activities of antioxidative enzymes with decreasing contents of lipid peroxide and H2O2. We infer that under the aerobic condition, enhancement of PAs and PAO activity enabled rice cultivars to tolerate oxidative stress, while under the transplanting condition, antioxidative defence system with decreasing of lipid peroxide content was closely associated with the protection of flag leaf by maintaining membrane integrity. In crux, results indicated that H2O2 metabolic machinery was strongly up-regulated especially at the anthesis stage.