An automated biogas fermenter running continuously for about two years using fodder and sugar beet silage as mono‐substrate without manure addition was analyzed simultaneously by amplified ribosomal DNA restriction analysis and microscopy. In this long‐term fermentation study, an oscillating population of prokaryotes was observed. The presence of most bacteria expected to be involved in hydrolysis of biomass via the anaerobic food chain was confirmed. In any case the methanogen population appeared more stable as it exhibited a lesser degree of variability. The more fluctuating population structure of the bacteria might be due to the fact that most of them were carbohydrate fermenting species which were therefore somewhat interchangeable. Hydrogenotrophic methanogens using H2+CO2 as substrate (Methanobacteriales and Methanomicrobiales) clearly dominated. Therefore, the methanogenesis of energy crops is apparently initiated by gasification to H2+CO2 followed by the biogasification to CH4+CO2. Acetotrophic methanogens (Methanosarcinales) represented a minority with a proportion of 10% or less of the methanogenic population (only at 55°C). The acetotrophic Methanosaeta seemed to be completely absent at temperatures of 55 or 60°C. Pure culture studies established previously that Methanobacteria tolerate at least a sixfold higher ammonium concentration (6000 mg/L) than Methanosaeta and a twofold higher ammonium concentration than Methansarcina. This indicates that running industrial scale fermenters at thermophilic instead of the common mesophilic conditions might be an effective way to exclude the more stress susceptible (e.g. high concentration of ammonium, H2S and acetate) acetotrophic methanogens and therefore improve the reliability of such plants.