Anaerobic ammonium oxidation (anammox), a reaction oxidizing ammonium to dinitrogen gas with nitrite as the electron acceptor under anoxic conditions, is one of the most recent discoveries in the biogeochemical nitrogen cycle. The anammox reaction is mediated by anammox bacteria, a deep-branching monophyletic group of bacteria within the phylum Planctomycetes. Presently, five genera and eight species of anammox bacteria have been identified, including Candidatus 'Brocadia’ (C. 'Brocadia anammoxidans’ and 'Brocadia fulgida’), C. 'Kuenenia stuttgartiensis’, C. 'Scalindua’ (C. 'Scalindua brodae’, 'Scalindua wagneri’ and 'Scalindua sorokinii’), C. 'Anammoxoglobus propionicus’ and C. 'Jettenia asiatica’. The anammox reaction takes place inside the anammoxosome, an intracytoplasmic compartment bounded by a single ladderane lipid-containing membrane. This unique cell structure has been found in all identified anammox bacteria. Although, there is no agreement on the biochemical mechanism of the anammox reaction, nitric oxide (NO) and hydrazine (N₂H₄) are recognized as important intermediates in the anammox reaction. The NO can oxidize ammonium to N₂H₄, and the N₂H₄ generated can be oxidized to dinitrogen gas by a hydrazine-oxidizing enzyme. The anammox process was first observed in a wastewater nitrogen-removal system, and seven of the eight anammox species were found in different wastewater treatment systems. Subsequently, many studies have reported the ubiquitous distribution of anammox bacteria in a variety of natural ecosystems, including anoxic marine sediments and water columns, marine oxygen-minimum zones, estuarine sediments, freshwater sediments and soil ecosystems. Anammox bacteria and their activities were also detected in several special ecosystems, such as high-temperature and low-temperature ecosystems. All available evidence indicates that the anammox process is critically important in natural ecosystems, and particularly in marine environments. In anoxic marine sediments and water columns, the anammox bacteria can account for 20%-79% and 20%-50% of total dinitrogen gas production, respectively. Anammox bacteria are also mainly responsible for nitrogen loss in the marine oxygen-minimum zones that are the most productive regions of the world's oceans. Anammox activities have been detected in freshwater and soil ecosystems but the specific contribution of anammox to the nitrogen cycle is poorly known and needs further investigation. Although anammox bacteria are broadly distributed in a variety of natural ecosystems, the overall diversity of anammox bacteria is low. The anammox bacteria detected in most marine and freshwater ecosystems are all affiliated with the genera C. 'Scalindua’ or 'Brocadia’. Recently, different anammox bacterial communities composed of C. 'Brocadia’, 'Kuenenia’, 'Scalindua’ and 'Jettenia’ species were found simultaneously in some estuarine and soil ecosystems, which expanded knowledge of the diversity of anammox bacteria in natural ecosystems. The different levels of anammox bacterial diversity and contribution of anammox to the nitrogen cycle observed in different natural ecosystems indicate that the anammox process is influenced by local environmental conditions. The organic content, availability of water column NO^-₃ or NO^-₂, salinity and temperature are regarded as the most important environmental factors influencing the anammox process in different natural ecosystems. This review summarizes the classification, biochemical mechanism, distribution and diversity of anammox bacteria in natural ecosystems, the importance of anammox in the global nitrogen cycle and the main factors influencing the anammox process in natural habitats.