Methane (CH₄) is the second most important greenhouse gas. Flooded rice fields are a major source of atmospheric CH₄, accounting for 5%-19% of total global emissions. Methanotrophs are the only known microorganisms that catalyze the oxidation of CH₄ produced in the rice fields and thus play an important role in attenuating the emissions of CH₄ into the atmosphere. Atmospheric CO₂ concentration has increased drastically and is predicted to double by the end of this century. This dramatic change in atmospheric CO₂ may have profound ecological consequence on biogeochemical cycles of key elements such as methane oxidation in rice fields. Free air CO₂ enrichment (FACE) is an ideal technique to assess ecosystem responses to the projected atmospheric CO₂ elevation by 2100 because it provides undisturbed field conditions and more reliable measurements than closed chambers with elevated CO₂. The effect of elevated atmospheric CO₂ on microbial methane oxidation has been investigated mostly by traditional techniques such as most probable number (MPN), which may underestimate the changes in methanotrophic changes under elevated CO₂. China-FACE was established in 2004 to investigate agricultural ecosystem response to simulated global change of rising atmospheric CO₂, and could approach the in situ conditions as much as possible for investigating the microbial mechanisms underlying methane oxidation changes under elevated CO₂. The rhizospheric soils at different rice growing seasons were collected to quantify the changes in methanotrophic populations using real-time quantitative PCR of pmoA genes of type Ia, type Ib and total methanotrophs. Pairwise comparison demonstrated positive responses of methanotrophic population size to elevated CO₂ at most stages of rice growing seasons. Total methanotrophs abundance were stimulated at the seedling and tillering stages in 2009, and seedling, jointing and grain filling stages in 2010 regardless of the application rates of nitrogenous fertilizer. In 2009, the total methanotrophs abundance was elevated at the ripening stage and declined at the flowering stage under high application rate of nitrogenous fertilizer, while the reverse trend was observed with regard to the low application rate of nitrogenous fertilizer. This implies that the availability of nitrogenous fertilizers might have intensified the response of methanotrophic populations to elevated CO₂ in rice field. A significant decline (P<0.1) in total methanotrophic population was observed at the ripening stage in 2010,suggesting that the elevated CO₂ inhibits the growth of methanotrophs under certain conditions. The consistent response to elevated CO₂ was observed for both type Ia and total methanotrophic population during rice growing seasons except for the tillering stage under low application rate of nitrogenous fertilizer in 2009. Type Ⅰb methanotrophic abundance was increased at most rice growing stages except for the grain filling stage under high application rate of nitrogenous fertilizer and the ripening stage under low application rate of nitrogenous fertilizer in 2010. Furthermore, high application rate of nitrogenous fertilizer further stimulated the abundance of type Ⅰ methanotrophs under elevated CO₂. This result implies that intensive fertilization appeared to favor the growth of type Ⅰ rather than type Ⅱ methanotrophs under elevated CO₂ condition. The results of this study suggested that the rising CO₂ concentration in the atmosphere may affect the community structure of methanotrophs, which could ultimately alter the biogeochemical methane cycling in rice fields.