In mature Phragmites australis and Scirpus lacustris vegetated sediment methane was emitted almost exclusively by plant-mediated transport, whereas in unvegetated, but otherwise identical sediment, methane was emitted almost exclusively by ebullition. Diel variations in methane emission, with highest emission rates at daytime and emission peaks following sunrise, were demonstrated for Phragmites and Scirpus. The diel difference and magnitude of the emission peaks were much smaller for Scirpus than for Phragmites. In contrast to Phragmites, methane concentrations within Scirpus stems did not change significantly over the diel period. These patterns are consistent with a two-way transport mechanism for Phragmites (convective at daytime and diffusive at night-time) and an all day diffusive mechanism for Scirpus. The patterns could not be accounted for by diel variation in air and sediment temperature, plant transpiration, or photosynthetically coupled methane production. Comparison of the experimentally derived ratio of methane emission in helium and nitrogen under light and dark conditions with the theoretical derived ratio (calculated according to the kinetic theory of gases) confirmed the exploitation of the different transport mechanism for Phragmites and Scirpus. Methane emission from Phragmites correlated significantly with incident light, which probably drove the pressure differential associated with thermally induced convection. Decrease of the radial resistance of Scirpus stems for methane transport under light compared to dark conditions, in combination with morphological characteristics of the plant species, suggested that stomatal aperture, regulated by light, controls methane emission from Scirpus. Diel variation in bubble emission from the non-vegetated sediment coincided with sediment temperature changes. The results have important implications for sampling and scaling strategies for estimating methane emission from wetlands.