Specific management of water regimes, soil and N in China might play an important role in regulating N2O and CH4 emissions in rice fields. Nitrous oxide and methane emissions from alternate non-flooded/flooded paddies were monitored simultaneously during a 516-day incubation with lysimeter experiments. Two N sources (15N-(NH4)2SO4 and 15N-labeled milk vetch) were applied to two contrasting paddies: one derived from Xiashu loess (Loess) and one from Quaternary red clay (Clay). Both N2O and CH4 emissions were significantly higher in soil Clay than in soil Loess during the flooded period. For both soil, N2O emissions peaked at the transition periods shortly after the beginning of the flooded and non-flooded seasons. Soil type affected N2O emission patterns. In soil Clay, the emission peak during the transition period from non-flooded to flooded conditions was much higher than the peak during the transition period from flooded to non-flooded conditions. In soil Loess, the emission peak during the transition period from flooded to non-flooded conditions was obviously higher than the peak during the transition period from non-flooded to flooded conditions except for milk vetch treatment. Soil type also had a significant effect on CH4 emissions during the flooded season, over which the weighted average flux was 111 mg C m-2 h-1 and 2.2 mg C m-2 h-1 from Clay and Loess, respectively. Results indicated that it was the transition in the water regime that dominated N2O emissions while it was the soil type that dominated CH4 emissions during the flooded season. Anaerobic oxidation of methane possibly existed in soil Loess during the flooded season. Specific management of water regimes, soil and N in China might play an important role in regulating N2O and CH4 emissions in rice fields. Nitrous oxide and methane emissions from alternate non-flooded / flooded paddies were monitored simultaneously during a 516-day incubation with lysimeter Two N sources (15N- (NH4) 2SO4 and 15N-labeled milk vetch were applied to two contrasting paddies: one derived from Xiashu loess (Loess) and one from Quaternary red clay (Clay). Both N2O and CH4 emissions were For both soil, N2O emissions peaked at the transition periods shortly after the beginning of the flooded and non-flooded seasons. Soil type affected N2O emission patterns. In soil Clay, the emission peak during the transition period from non-flooded to flooded conditions was much higher than the peak during the transition period from flooded to non-flooded conditions. In soil Loess, the emission peak dur ing the transition period from flooded to non-flooded conditions was obviously higher than the peak during the transition period from non-flooded to flooded conditions except for milk vetch treatment. which the weighted average flux was 111 mg C m-2 h-1 and 2.2 mg C m-2 h-1 from Clay and Loess, respectively. Results indicate that it was the transition in the water regime that dominated N2O emissions while it was the soil type that dominated CH4 emissions during the flooded season. Anaerobic oxidation of methane possibly existed in soil Loess during the flooded season.