Identifying the optimal rice establishment option combined with specific fertilizer application can lower the global warming potential (GWP) and greenhouse gases intensity (GHGI) of rice production. In this study, methane (CH4) and nitric oxide (N2O) emissions and rice yields under different fertilizer application methods and two different planting methods, transplanted rice (TPR) and wet bed direct seeded rice (WDSR), was measured. Field experiments using a split plot design and closed chamber-GC method for gas flux measurements were conducted. CH4 and N2O emissions ranged from 1.83-4.68 mg/m2/h and 0.073-0.135 mg/m2/h, respectively. Minimum CH4 and N2O emissions were observed at 48-69 days after seedling (DAS) (tiller stage), while maximum emissions were generally found at 90 DAS or early primordial initiation (EPI) stage. It was found that TPR produced more CH4 and N2O than WDSR across fertilizers methods almost each growth stage throughout the growing period. Regarding GHGs emission factors, CH4 emissions were negatively correlated with soil pH (-0.35*, N=18). At higher soil pH, lower CH4 emissions were found in early growth stages. The N2O emissions did not correlate with soil pH (-0.04 ns, N=18). The highest average CH4 emission was reached in 90 days after seedling and EPI when the soil temperature was maximal at 34.8ºC. The correlation coefficient (r) between CH4 emission and soil temperature was 0.48*, N=18, indicating a positive correlation.