The aim of this experiment was to monitor the microbial communities in two biogas reactors and evaluate the efficiency of denaturing gradient gel electrophoresis (DGGE) as a technique for visualizing shifts in the microbial compositions. The reactors were followed from September 2011 to May 2012. The first reactor is a pilot scale upflow anaerobic sludge blanket (UASB) reactor situated at Foss farm outside of Porsgrunn, running on cow manure. The second reactor is lab scale and situated at Telemark University College, running on pig manure. Samples were taken from the reactors at regular intervals. DNA was extracted from the samples and amplified by polymerase chain reaction (PCR). The primers were 338f and 518r, targeting the 16S rDNA sequence. Changes in the microbial diversity were detected by DGGE in both reactors. Some bands appeared and other disappeared during the period. These changes could not be correlated to changes in operating conditions. This was probably because DGGE reflects cell amounts and not microbe activity levels. DGGE is a highly reproducible and consistently performing fingerprinting technique. It is capable of reflecting long term shifts in the microbial communities and several samples can be compared in one gel. This makes DGGE an effective method for monitoring reactors over time. Several DGGE bands were excised and sequenced, but the results were either negative, or of too poor quality, for further analysis. The probable cause was insufficient separation of bands leading to multiple sequences in the extracted DNA. This may be overcome by using a more specific primer set to reduce the amount of bands.