The present work establishes intermittent operation of UASB reactors as a novel form of enhancing the anaerobic degradation of complex wastewaters and its conversion to usable biogas. Results show that the average methane production rate is 25% higher with the intermittent operation than with the continuous mode, meaning that it could produce 25% more electricity or heat. The methanization efficiency obtained in intermittent UASB reactors is around 20% higher than in the continuous systems, confirming a higher biological degradation of the substrates. It has been suggested that intermittent operation causes a forced adaptation of the biomass towards the degradation of complex substrates and results from morphological analyses of the biomass developed in intermittent and continuous UASB reactors showed marked differences between them. In order to gain a deeper knowledge on how microbial populations are affected by these operational parameters, a strategy involving the amplification, cloning, and analysis of the nucleotide sequences of genes encoding the 16S ribosomal RNA was undertaken and is described in this work. This strategy allowed the identification of a total of 49 different sequences. Results from the molecular characterization of the microbial populations are consistent with the higher methanization efficiency of the intermittent mode of operation.