The study is focused on impact of manure application, rice varieties and water management on greenhouse gas (GHG) emissions from paddy rice soil in pot experiment. The objectives of this study were a) to assess the effect of different types of manure amendments and rice varieties on greenhouse gas emissions and b) to determine the optimum manure application rate to increase rice yield while mitigating GHG emissions under alternate wetting and drying irrigation in paddy rice production. The first pot experiment was conducted at the Department of Agronomy, Yezin Agricultural University, Myanmar, in the wet season from June to October 2016. Two different organic manures (compost and cow dung) and control (no manure), and two rice varieties; Manawthukha (135 days) and IR-50 (115 days), were tested. The results showed that cumulative CH4 emission from Manawthukha (1.084 g CH4 kg-1 soil) was significantly higher than that from IR-50 (0.683 g CH4 kg-1 soil) (P<0.0046) with yield increase (P<0.0164) because of the longer growth duration of the former. In contrast, higher cumulative nitrous oxide emissions were found for IR-50 (2.644 mg N2O kg-1 soil) than for Manawthukha (2.585 mg N2O kg-1 soil). However, IR-50 showed less global warming potential (GWP) than Manawthukha (P<0.0050). Although not significant, the numerically lowest CH4 and N2O emissions were observed in the cow dung manure treatment (0.808 g CH4 kg-1 soil, 2.135 mg N2O kg-1 soil) compared to those of the control and compost. To determine the effect of water management and organic manures on greenhouse gas emissions, second pot experiments were conducted in Madaya township during the dry and wet seasons from February to October 2017. Two water management practices {continuous flooding (CF) and alternate wetting and drying (AWD)} and four cow dung manure rates {(1) 0 (2) 2.5 t ha-1 (3) 5 t ha-1 (4) 7.5 t ha-1} were tested. The different cow dung manure rates did not significantly affect grain yield or greenhouse gas emissions in this experiment. Across the manure treatments, AWD irrigation significantly reduced CH4 emissions by 70% during the dry season and 66% during the wet season. Although a relative increase in N2O emissions under AWD was observed in both rice seasons, the global warming potential was significantly reduced in AWD compared to CF in both seasons (P<0.0002, P<0.0000) according to reduced emission in CH4. Therefore, AWD is the effective mitigation practice for reducing GWP without compromising rice yield while manure amendment had no significant effect on GHG emission from paddy rice field. Besides, AWD saved water about 10% in dry season and 19% in wet season.