The dynamics of bacterial and archaeal populations of a laboratory-scale anaerobic digestor were investigated during a crisis period of the process reflected by an accumulation of acetate. A culture-independent approach based on single strand conformation polymorphism (SSCP) analysis of total 16S rDNA and 16S rRNA amplification products was used. A spirochete and a Synergistes sp. showed high and changing activity levels during the study. A Clostridium sp. showed a transient increase in presence and activity concomitant with the highest acetate concentrations. A major shift in the most active archaeal populations from hydrogenotrophic to acetoclastic methanogens preceded the recovery of the reactor.