Aerobic methanotrophs (MOB) are a functional group of proteobacteria that use methane as their only energy and carbon source. Phylogenetically, such methanotrophs are affiliated with present alpha and gamma proteobacteria. Methanotrophic microorganisms play an essential role in the methane cycle, since they to a great extent reduce potential methane emissions to the atmosphere. In stratified lakes the aerobic methanotrophs are commonly present at the oxic-anoxic interfaces. This study aims to identify the environmental factors that could regulate the distribution of aerobic methanotrophs in the water column of freshwater lakes as well to assess whether a vertical community structure exists there. Lakes Erken and Tämnaren located in central Swedenwere studied using molecular analysis and environmental data. Aerobic methanotrophs were detected throughout the water column of Lake Erken. Two types of methanotroph communities were identified, with distribution patterns that appeared to be correlated to levels of methane in the water. Furthermore one of these communities feature changes in the relative abundance of its member populations along a depth gradient suggesting further differentiation along chemical gradients in the hypolimnion. Sequencing of pmoA amplicons revealed only members of the gamma proteobacteria methanotrophs. Also two novel operational taxonomic units were identified. Methanotrophs communities between Tämnaren and Erken also differ. Together these results indicate the existence of distribution patterns in methanotroph freshwater communities.