Biomethane has gained increasing attention in the recent years as an alternative, local energy source option. Biogas is generated during the anaerobic digestion of organic materials via a multistep process catalyzed by complex microbial communities. This review aims at providing a concise summary of recent studies on the microbial communities in various biogas reactors. The effects of acid composition, C/N ratio, mixing and the geometry of the anaerobic digester on the microbial ecosystem are discussed. The biogas microbial communities show extensive fluctuations in response to changes in temperature, substrate type, pH, type of volatile fatty acids, organic loading rate, etc. The goals to ensure efficient anaerobic degradation and to maximize the biogas production require the better understanding of these bacterial-archaeal ecosystems, since functional stability strongly correlates with the state and composition of microbial communities. The safe and controlled intensification of biogas production would be an important step to make biogas a real competitor of fossil fuels.