The main purpose of this study was to optimize the methods for determining methane emission in a continuously flooded (CF) and an alternately wetted and dried rice system. A field experiment was conducted at Block B1, Pili Drive, Los Baños, Laguna for one cropping season to evaluate the CH4 emission in both FP and AWD treatment plots. Fertilizer application rates were similar across treatments and were based on the recommended rate. Gas sampling was done weekly at 0, 15, and 30-minute intervals and was analyzed using a gas chromatograph equipped with a flame-ionization detector (FID). Results showed that FP plots emitted methane at 15.07 to 459.14 mg CH4 day-1 m-2, which was higher than those produced in AWD plots which ranged from 1.68 to 36.26 mg CH4 day-1 m-2 throughout the cropping period. In both treatments, a decreasing trend in methane emission was observed which was attributed to the depleting carbon source of methanotrophs where methane was utilized rather than produced at an unfavorable redox potential for methane production. Global warming potential (GWP) of were 7,000 kg CO2-eq and 1,350 kg CO2-eq was contributed by FP and AWD treatments, respectively. Overall, CH4 emission was reduced by 80-85% when AWD was employed without having a yield compromise. The result of this pilot study is limited to a 1,300 m2 field area but it showed a significant comparison between the two water management strategies in rice systems. Also, the learnings in this study will be used further for landscape greenhouse gas measurements in major rice-producing areas in the Philippines and ultimately will contribute to the carbon footprint assessment of rice cultivation.