Two Italian rice (Oryza sativa var. japonica) cultivars, Lido and Roma, were tested in the field for methane production, oxidation and emission. In two consecutive years, fields planted with the rice cultivar Lido showed methane emissions 24–31% lower than fields planted with the cultivar Roma. This difference was observed irrespective of fertilizer treatment. In contrast to methane emissions, differences in methane production or oxidation were not observed between fields planted with the two cultivars. Plant-mediated transport of methane from the sediment to the atmosphere was the dominating pathway of methane emission. During the entire vegetation period, the contribution of this pathway to total methane emission amounted to c. 90%, whereas the contribution of gas bubble release and of diffusion through the water column to total methane emission was of minor significance. Results obtained from transport studies of tracer gas through the aerenchyma system of rice plants demonstrated that the root–shoot transition zone is the main site of resistance to plant-mediated gas exchange between the soil and the atmosphere. The cultivar Lido, showing relatively low methane emissions in the field, had a significantly lower gas transport capacity through the aerenchyma system than the cultivar Roma. Thus, the observed differences in methane emissions in the field between the cultivars Lido and Roma can be explained by different gas transport capacities. Apparently, these differences in gas transport capacities are a consequence of differences in morphology of the aerenchyma systems, especially in the root–shoot transition zone. It is, therefore, concluded that identification and use of high-yielding rice cultivars which have a low gas transport capacity represent an economically feasible, environmentally sound and promising approach to mitigating methane emissons from rice paddy fields.