Greenhouse experiments were conducted under subtropical conditions to understand the mechanism of rice cultivar differences in methane (CH4) emission. Three rice cultivars were studied. Differences in CH4 emission rates among the three rice cultivars became evident in the middle and late growth stages. Rice root exudates per plant measured as total released C were significantly different among rice cultivars. The effect of root exudates on CH4 production in soil slurry differed accordingly. The amount of root exudates was not significantly different among rice cultivars when computed on a dry matter basis, indicating that it is positively correlated to root dry matter production. The root CH4-oxidizing activity differed among rice cultivars. IR65598 had a higher oxidative activity than IR72 and Chiyonishiki. Root air space was not significantly different among rice cultivars at the late growth stage, indicating that it is probably not a factor contributing to cultivar differences in CH4 emission. The population level of methanogenic bacteria differed significantly in soil grown to different rice cultivars, but not in roots, at booting stage and ripening stage. Methanotrophic bacteria population differed significantly in roots among rice cultivars at ripening. Rice cultivars with few unproductive tillers, small root system, high root oxidative activity, and high harvest index are ideal for mitigating CH4 emission in rice fields.