Plant-mediated transport is the primary route of methane (CH(4)) emission from the reduced paddy field to the aboveground atmosphere. Experiments were conducted at North Bank Plain Agro-climatic Zone of Assam, India, during monsoon rice-growing season (July to December 2006) to elucidate the influences of anatomical and morphophysiological characteristics of rice (Oryza sativa L.) cultivars on methane emission from submerged agroecosystem. Ten rice cultivars were grown in light-textured loamy soil under rainfed uniform field condition. Among the 10 cultivars, 5 were traditional rice genotypes commonly grown in the agroclimatic zone and the other 5 were improved high-yielding varieties. Wide variation in CH(4) flux was recorded among the rice cultivars, which may be regulated by the difference in anatomical and morphophysiological characteristics of rice plant. Microscopic analysis of stem portion showed that high- and medium-CH(4)-emitting cultivars recorded higher size of the medullary cavity. Leaf area and transpirational rates were also found to be higher in high-CH(4)-emitting varieties. Scanning electron microscopic analysis revealed higher stomatal frequencies in high-methane-emitting cultivars. Data presented in this study suggest that variation in anatomical and morphophysiological characteristics among different rice genotypes may influence CH(4) emission from paddy fields.