Methanogens are known to inhabit not only the anaerobic bulk soil but also the rhizosphere of rice plants. The release of root exudates, a major carbon source for CH4 production in the rhizosphere, is closely coupled to plant photosynthesis. In the present study we hypothesized that the diel cycle of plant photosynthetic activity may shape the structure and function of methanogens in the rhizosphere of rice. We performed a field experiment to determine the diel dynamics of methanogen mcrA and their transcripts in the rhizosphere and bulk soil. The chemistry of NH4+, NO3−, SO42− and Fe(II) in the rice rhizosphere remained constant over a diel sampling. The mcrA copy number and their transcripts were greater in the rice rhizosphere compared with the bulk soil, indicating the enhanced activity of methanogens in the rhizosphere. The hydrogenotrophic Methanomicrobiales in particular increased in the rhizosphere whereas Methanosarcinaceae were more abundant in the bulk soil. Both the phylogenetic affiliation and copy numbers of methanogen mcrA in the rice rhizosphere did not display diel dynamics. The mcrA transcripts, however, significantly increased in the night compared with the daytime. The diel pattern of physical factors like temperature appeared not to affect the methanogen dynamics. The response of mcrA transcripts is probably due to the plant attributes, which release less O2 from roots in the night and hence stimulate the methanogen gene transcription and activity compared with the daytime.