Abstract Lake ecosystems contribute significantly to atmospheric methane and are likely to become even bigger methane emitters with the global spread of hypoxia/anoxia in freshwater ecosystems. Here we characterized the spatial heterogeneity of methane production potential, methane concentration, archeal and bacterial communities across Lake Remoray sediment during the summer period when hypoxic conditions settle in the deepest part of the water column. It was hypothesized that methane concentration and production would be higher in the deeper part of the lake, our results showed that some littoral areas exhibited similar or higher values than the deepest area. The full 16S rRNA gene sequencing dataset counted 41 OTUs affiliated with methanogenic species in abundances that depended more on sampling‐site location than on the water depth gradient. The methanogenic co‐occurrence network revealed the existence of five distinct sub‐communities, suggesting the presence of different methanogenic niches across Lake Remoray. The variation in abundance of the two larger methanogenic sub‐communities was significantly related to methanogenesis potential and sediment methane concentration across‐lake but further studies investigating their real activities would provide additional insights. In a globally changing environment (temperature, eutrophication, …) a better understanding of the functional specificities and characteristics of the potential of methane cycle actors would allow us to better predict their future implications for greenhouse gas production and mitigation.