In lake ecosystems a major proportion of methane emissions originate from the littoral zone which can have a great spatial variability in hydrology, soil quality and vegetation. Hitherto, spatial heterogeneity and the effects it has on functioning and diversity of methanotrophs in littoral wetlands is poorly understood. A diagnostic microarray based on the particulate methane monooxygenase gene coupled with geostatistics was used to analyze spatial patterns of methanotrophs in the littoral wetland of a eutrophic boreal lake (Lake Kevätön, Eastern Finland). The wetland had a hydrology gradient with mean water table varying from −8 cm to −25 cm. The wettest area comprising the highest methane oxidation, had the highest abundance and species richness of methanotrophs. High water table favoured the occurrence of type Ib methanotrophs whereas type Ia and type II were found under all moisture conditions. Thus the spatial heterogeneity in functioning and diversity of methanotrophs in littoral wetlands is highly dependent on water table which in turn varies spatially in relation to the geomorphology of the wetland. We suggest that changes in water levels resulting from regulation of lakes and/or global change will affect the abundance, activity, diversity of methanotrophs and consequently methane emissions from such systems.