Wastewater treatment based on activated sludge is known to be one of the most effective and popular wastewater purification methods. An estimation of microbial community variability in activated sludge allows us to observe the correlation between a particular bacterial group's appearance and the effectiveness of the removal of chemical substances. This research is focused on microbial community temporal changes in membrane bioreactors treating wastes containing a high level of ammonia nitrogen. Samples for this study were collected from two membrane bioreactors with an activated sludge age of 12 and 32 days, respectively. The activated sludge microbial community was adapted for the removal of ammonia nitrogen up to a level of 0.3 g NH4(+) - N g/VSS/d (VSS - volatile suspended solids). The methods - denaturing gradient gel electrophoresis (DGGE) based on 16S rRNA gene PCR products and fluorescent in situ hybridization (FISH) with 16S rRNA gene probes - revealed significant differences in the microbial community structure in the two bioreactors, caused mainly by a difference in sludge age. According to the results obtained in this study, a bioreactor with a sludge age of 12 days is characterized by a much higher microbial community diversity than a bioreactor with a sludge age of 32 days. Interestingly, the appearance of particular species of nitrifying bacteria was constant throughout the experiment in both bioreactors. Changes occured only in the case of the Nitrosomonas oligotropha lineage bacteria. This study demonstrates that the bacterial community of bioreactors operating with different sludge ages differs in total community structure. Nevertheless, the changeability of the bacterial community structure did not have any influence on the efficiency of nitrification.