The presence of aerobic anoxygenic phototrophs (AAPs) has been repeatedly reported from various marine environments, but their distribution in freshwater lakes was neglected until recently. We investigated the phylogenetic composition of AAP communities in 10 lakes in Northeastern Germany with different trophic status including oligotrophic Lake Stechlin and humic matter rich Lake Grosse Fuchskuhle. The AAP community was composed by members of Alpha- and Betaproteobacteria, but their contribution varied largely among the studied lakes. Our results show that AAP community composition in the studied lakes was affected mostly by pH and humic matter content. While alkaline lakes were mostly composed of Betaproteobacteria, the acidic and humic matter rich south-west (SW) basin of Lake Grosse Fuchskule was dominated (87%) by Alphaproteobacteria. The most frequent group within Betaproteobacteria was a cluster of pufM genes which was phylogenetically related to Rhodoferax representing 38.5% of all retrieved sequences. Alphaproteobacteria-related sequences had a broader phylogenetic diversity including six different taxa dominated by Sphingomonas- and Rhodobacter-like bacteria in lakes with alkaline to neutral pH. In the acidic and humic matter-rich SW basin of Lake Grosse Fuchskuhle, however, Methylobacterium-related sequences dominated the AAP community. We suggest that the variable AAP community structure might reflect the potential of these bacteria to cope with the contrasting conditions in freshwater environments.