Many studies have examined greenhouse gas fluxes from rice paddies, but information about microorganisms involved in the process is limited. In this study, we used a molecular approach to identify functional genes including mcrA, pmoA, and nirK/nirS/nosZ to quantify the abundance of methanogens, methane-oxidizing bacteria, and denitrifiers, respectively. We also analyzed soil chemical properties such as soil organic matter, pH, and inorganic nitrogen to detect key variables, which control the abundances of these microbes. Abundances of methanogens, methane-oxidizing bacteria, and denitrifying genes were unchanged during the 1-year study. The abundances of methane-oxidizing bacteria and denitrifiers, except for methanogens, were highest near the soil surface where oxygen availability was likely higher. It is noteworthy that genes for the reduction of CH4 and N2O were particularly abundant near the soil surface. Additionally, most of gene abundances were correlated with SOM and inorganic nitrogen especially during summer. Overall, the results indicated that nicrobes responsible for CH4 or N2O dynamics were not affected by seasons, but were sensitive to oxyen availability and soil chemical properties. We also concluded that GHG emission would be stimulated by increased C availability and microbial activities in rice paddies, which are expected to be enhanced by global climate change.