Anaerobic sludge stabilization is a commonly used technology. Most fermenters are operated at a mesophilic temperature regime. Modern trends in waste management aim to minimize waste generation. One of the strategies can be achieved by anaerobically stabilizing the sludge by raising the temperature. Higher temperatures will allow faster decomposition of organic matter, shortening the retention time, and increasing biogas production. This work is focused on the description of changes in the community of methanogenic microorganisms at different temperatures during the sludge stabilization. At higher temperatures, biogas contained a higher percentage of methane, however, there was an undesirable accumulation of ammonia in the fermenter. Representatives of the hydrogenotrophic genus Methanoliea were described at all temperatures tested. At temperatures up to 50 °C, a significant proportion of methanogens were also formed by acetoclastic representatives of Methanosaeta sp. and acetoclastic representatives of the order Methanosarcinales. The composition of methanogens in the fermenter significantly changed at 60 °C when typically thermophilic species, like Methanothermobacter marburgensis, appeared. A decrease in the diversity of methanogens was observed, and typical hydrogenotrophic methanogenic archaea isolated from fermenters of biogas plants and anaerobic wastewater treatment plants represented by genus Methanoculleus were no longer present.