Microbial community shifts were determined by denaturing gradient gel electrophoresis (DGGE) and real-time PCR for an anaerobic batch digester treating secondary sludge. The batch process was successfully operated with an organic removal efficiency of 35% associated with a 91% decrease in the bacterial 16S rRNA gene concentration. The microbial community structures showed continuous shifts within four bacterial phyla and three archaeal orders. Several bacterial species, such as Fusibacter-related, Clostridium-like, and Syntrophus-like organisms, appeared to be responsible for acidogenesis or syntrophic acid degradation. Both hydrogenotrophic and aceticlastic methanogens appear to have been involved in the methanogenesis with the acidogenic products. The quantitative structure of the methanogenic populations varied continuously, with the growth of Methanomicrobiales and Methanosarcinales in series, to result in a Methanomicrobiales-dominant population. The ordination of microbial community structures demonstrated that the quantitative methanogenic structure converged to the seed inoculum while the bacterial and archaeal DGGE band patterns diverged. These results provide an insight into the microbial behavior in the transitional phase (e.g., a start-up period) of anaerobic sludge digestion. (C) 2010 Elsevier Ltd. All rights reserved.