Nitrification is an important factor in the global nitrogen cycle. Therefore, an increasing number of publications deal with in situ studies of natural bacterial populations participating in this process. However, some crucial points complicate suchlike investigations. At the time being, a total of 25 species of ammonia-oxidizers and eight species of nitrite-oxidizers are cultured but the existence of many more species has been indicated by molecular in situ investigations. With that, only a part of the existing nitrifiers has been defined via isolation and subsequent physiological and molecular characterization. Furthermore, the distribution patterns of the distinct species of nitrifiers depend on various environmental parameters. Hence the composition of nitrifying bacterial communities is complex and divers in heterogeneous habitats. In consequence of the above-mentioned problems, the representation of nitrifying community structures obtained from in situ investigations often has been incomplete and unbalanced in many respects. Polyphasic approaches, applying a combination of classical as well as molecular methods in parallel, could help to find the way for overcoming these problems in the future. Isolation and characterization of as many as possible new species seems to be one of the most important missing steps to advance at this way.