At the ecosystem and global scales, the carbon isotopic compositions of CO2 and methane exchanged between the biosphere and the atmosphere (delta(N), and delta(M), respectively) have been used to partition net fluxes of CO2 and methane into the source and sink terms. The temporal variations of delta(N) and delta(M) were investigated at the same time in a Japanese rice paddy by combining stable isotopes and concentration measurements within and above the canopy. There were close agreements between the measured concentrations and the delta C-13 values of CO2 and methane on both temporal and spatial scales. While atmospheric stability and environmental parameters influencing photosynthetic assimilation were the major controls on variability of [CO2] and delta(CO2)-C-13, atmospheric stability was the predominant factor for driving changes in [CH4] and delta(CH4)-C-13 profiles. We also found strong linear relationships between the measured isotopic compositions and the inverse of concentrations over the time spans of day, night, and whole day. The delta(N) values determined on the two days contrasting in environmental conditions revealed that the relative contributions of photosynthetic assimilation and ecosystem respiration to the total CO2 exchange did not change significantly. In contrast, the delta(M) values showed a marked difference between the sampling dates, reflecting a transpiration-induced shift in methane transport.