The activity and community structure of methanotrophs was investigated in compartmented microcosms over the growth period of rice plants. In-situ methane oxidation was only important during the vegetative growth phase of the plants and later on became negligible. The in-situ activity was not directly correlated to methanotrophic cell counts, which increased further even after the decrease of in-situ activity, possibly due to the parallel detection of vegetative cells and resting stages. By dividing the microcosms into two soil and two root compartments it was possible to locate methanotrophic growth and activity, which was highest at the rhizoplane of the rice plants. Molecular analysis by denaturing gradient gel electrophoresis (DGGE) and fluorescent in-situ hybridisation (FISH) with family specific probes revealed the presence of both families of methanotrophs in soil and root compartments over the whole season. Changes in community structure were detected solely for Methylococcaceae, and could only be affiliated to changes within the genus Methylobacter and not to changes in the dominance of different genera in this family. For Methylocystaceae a stable community in all compartments and over the whole season was observed. FISH analysis revealed evidence for the in-situ dominance of Methylocystaceae in all compartments. Methylococcaceae showed high relative cell numbers only in the rhizoplane, demonstrating the importance of the rice roots for growth and maintenance of methanotrophic diversity in the soil.