Ammonia oxidation by autotrophic ammonia-oxidizing bacteria (AOB) is a key process in agricultural soils, wastewater treatment and natural ecosystems and plays an important role in the global nitrogen cycle. With the advent of cultivation-independent molecular biotechnologies, significant research progress has been made in understanding the ecology, phylogeny and distribution of AOB. These bacteria are widely distributed in nature and are found in soils, sand dunes, biofilms, fluidized bed reactors, lakes, wastewater, and seawater. The 16S rRNA gene is the chief phylogenetic marker that has been used for elucidating AOB evolution. Recent studies have demonstrated that there is a high consistency between phylogenetic trees based on the 16S rRNA gene and those based on ammonia monooxygenase gene (amoA) sequences. The amoA gene codes for a functional protein that is involved directly in ammonia oxidation and, therefore, a considerably higher number of differences in amoA gene sequences derived from different AOB are expected. Thus, using amoA as a marker is expected to increase the resolving power in the study of AOB diversity in the environment as compared to 16S rRNA-based markers. Recent studies have also revealed that the distribution of AOB is affected by different environmental conditions. Ammonium availability, acidity, dissolved oxygen, temperature, and salinity have all been shown to selectively affect, to some extent, the number of AOB species and the abundance of AOB in various environments. The ability of certain AOB to grow at continuously low ammonium and oxygen concentrations and to become active again after longer periods of starvation allows these bacteria to better exploit irregular pulses of ammonium and oxygen in the environment and thus persist for longer periods of time. Ureolysis provides a mechanism for nitrification by AOB in acid soils. When urea enters the cells by diffusion, intracellular urea hydrolysis and ammonia oxidation occur independently of extracellular pH in the range 4 to 7.5, thus allowing them to overcome a major constraint to their activity at low pH. Here we describe our perspectives for the future research of AOB in applied ecology and environmental protection.