Permafrost thaw ponds in the subarctic region of Quebec emit net flux of methane to the atmosphere. Since microbial communities control biogeochemical processes, and in particular methane balance, understanding factors that influence archaeal 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 archaeal communities in subarctic thaw lakes across a gradient of limnological conditions and permafrost degradation.