In aquaculture, co-culturing rice with fish may mitigate greenhouse-gas emissions. In this study, co-culture of four rice cultivars in a laboratory-scale rice–fish system reduced CH4 and N2O emissions relative to fish monoculture. Differences in CH4 and N2O emissions among rice cultivars primarily stem from the differential effects of rice plants on plant-mediated CH4 transport, CH4 oxidation and nitrogen absorption.