Microbial communities display a variety of biogeographical patterns mainly driven by large-scale environmental gradients. Here, we analysed the spatial distribution of methane-oxidizing bacteria (MOB) and methane oxidation in a strongly fluctuating environment. We investigated whether the spatial variability of the MOB community can be explained by an environmental gradient and whether this changes with different plot sizes. We applied a pmoA-specific microarray to detect MOB, measured methane oxidation, methane emissions and soil properties. All variables were measured in a 10 × 10 m, 1 × 1 m and 20 × 20 cm plot and interpreted using a geostatistical approach. Methane oxidation as well as MOB displayed spatial patterns reflected in the underlying flooding gradient. Overlapping and contrasting spatial patterns for type I and type II MOB suggested different ecological life strategies. With smaller plot size, the environmental gradient could not explain the variability in the data and local factors became more important. In conclusion, environmental gradients can generally explain variability in microbial spatial patterns; however, we think that this does not contribute to a mechanistic explanation for microbial diversity because the relevant scales for microorganisms are much smaller than those normally measured.