In the process of treating waste water in biological treatment plants, the nitrification process is crucial for the removal of one of the most important nutrients, i.e. nitrogen, using nitrification bacteria. The aim of our work was to produce a study of the process of nitrification itself, including an analysis of the presence, diversity and stability of microbial communities based on the 16S rRNA sequences and specific functional genes (eg. amoA) in industrial-scale and laboratory-scale reactors with immobilized bioculture. Industrial-scale reactors treat wastewater of temporary variable composition under different weather conditions, while the microbial population of wastewater treatment plants are often studied in controlled laboratory-scale systems with defined influent at a constant temperature. 16S rRNA and ammonia oxidising amoA-gene-defined bacterial community structure was investigated in industrial-scale and laboratory-scale moving bes biofilm reactor (MBBR) treating municipial wastewater or synthetic ammonium solition. Nitrification activity, 16S rRNA and amoA gene TRFLP profiles were comparable between industrial and laboratory-scale reactors with municipial wastewater. Reactors with synthetic ammonium solution exhibited higher nitrification and higher relative abundance of Nitrosomonadaceae and Nitrospiraceae families but only small changes in general bacterial community structure was detected compared to MBBR reactors treating municipial wastewater. Nitrosomonas europea lineage dominated in reactors treating municipial wastewater, whilu uncultivated Nitrosomonas-like sequences prevailed in reactors with synthetic ammonia solution. These results suggest that influent type has a stronger influence on community structure than operational conditions, such as temperature or reactor size.