We used 454 pyrosequencing to determine the bacterial community composition of 29 permafrost thaw ponds over a North-South permafrost degradation gradient in subarctic Quebec (Canada). In addition, we sampled a set of reference lakes whose formation was not related to permafrost thawing. The ultimate objective was to investigate the spatial structure of bacterial communities and to identify the main community assembly processes at different spatial scales. In particular, we aimed at investigating whether differences in community composition mainly result from local adaptation to contemporaneous environmental conditions or reflect global warming induced changes.