Microbial assemblages in thaw ponds inhabit highly heterogeneous environments where physico-chemical conditions vary both vertically through the water column and spatially across permafrost regions. Since these microbial communities control biogeochemical processes, and in particular methane balance, understanding factors that influence bacterial community composition and assembly is central for predicting net greenhouse gas emissions from the thawing landscape. The goal of the present study was to investigate the diversity and distribution of potentially active bacterial communities in subarctic thaw lakes across a gradient of limnological conditions and permafrost degradation.