Methane (CH4) is one of the important greenhouse gases; it has 23-times stronger greenhouse effects than CO2. FACE (free air CO2 enrichment) experiment under paddy fields has been conducted in Shizukuishi, Iwate prefecture, Japan. In this experiment, atmospheric CO2 concentration was maintained at 200 ppm higher level than that of the control plots. We examined the relationships between CH4 flux from paddy fields and abundances of bacterial communities in soil. Soil samples were harvested from the midpoint of between-hills at four times (June 19, July 13, Aug 7 and Sep 3). DNAs of soil and root were extracted and abundances of methanogenic bacteria, methanotrophic bacteria and total bacteria in each of root and soil were examined by quantitative real-time PCR using specific primer for each member. CH4 emission showed clear seasonal pattern. It largely increased from July to August. Elevated CO2 did not increase CH4 emission, but elevated water temperature significantly increased CH4 emission. Methanogenic bacterial abundance in the root showed similar pattern with CH4 flux, but that in the soil did not show little change with harvests. Total bacterial abundance also showed similar pattern with methanogenic bacteria. These results suggest that the bacteria living in roots, not those in soil, are responsible for seasonal pattern of CH4 flux.