Abstract: The anaerobic ammonium oxidation (anammox) process occurring in the natural environment is a new pathway for nitrogen loss other than traditional denitrification and aerobic ammonia oxidation. Recent studies demonstrate a widespread presence of phylogenetically distinct anammox in the natural environment, suggesting its great significance to the global nitrogen cycle. In this paper, we reviewed the ecophysiological mechanism of anammox process; summarized the functional diversity of anammox microorganisms in different natural habitats; described the driving forces that might have shaped the heterogeneity of anammox bacteria across different scales. The key finding is that appropriate amount of inorganic nitrogen can promote the occurrence of anammox. It is more suitable for anammox bacteria and its activity under low organic carbon content and low oxygen conditions because of chemical autotrophic metabolic pathways. Since the activity of denitrifying bacteria is temporarily inhibited under low nutrient conditions, which promotes the appearance of anaerobic ammonium oxidation. Meanwhile, the relatively high salinity could likely result in the enhanced activity and the shift of anammox bacteria communities. Scalindua is dominant in relatively high salinity environment, but Brocadia is common in low salinity environment. Anammox bacteria could have great potential for adaption to different temperature in the environment, most anammox bacteria such as Scalindua, Kuenenia and Brocadia have strong adaptability to extreme environments. In addition, the concentration of suspended particles and water volume play an important role in determining the community structure and activity of anammox bacteria. In the future, we can combine genomics and proteomics with transcriptomics to study the physiological ecology mechanisms of anammox bacteria in the natural environment, and find out the biochemical relationship between anammox process and the factors such as Fe³⁺, Mn⁴⁺ and SO₄^2- under anaerobic conditions, in order to apply it to engineering technology and to provide a theoretical basis for ecological environment restoration.