Use of nitrifying and denitrifying bacteria to remove ammonia from waste water had been studied for a long time due to their high efficiency and low cost. Nitrifying bacteria not only grow slowly but also require high concentration of oxygen to facilitate the nitrifying process. Moreover, the followed denitrifying process needs the supply of adequate carbon sources for denitrifying bacteria to avoid greenhouse gas emission from the system. It shows the operational control to remove ammonia from waste water would be very difficult. Therefore, it is important to study the physiological and biochemical characteristics of those nitrifying and denitrifying bacteria closely. In 1995, Mulder discovered the disappearance of ammonium at the expense of nitrate and nitrogen production from their denitrifying pilot plant in the Netherlands, then van de Graaf verified an ANAMMOX reaction in the laboratory. Further studies that have revealed the combination of aerobic nitrification and anaerobic ammonium oxidation is more efficient to remove ammonia than most conventional methods. The ANAMMOX process is performed by a group of Planctomycete which involves the oxidation of ammonia anaerobically with nitrite as the final electron acceptor to yield gaseous nitrogen. Since this process is no need of supply external carbon source and oxygen, the ANAMMOX system can offer the advantages of less cost, less microbial contamination and less N2O and NO emission to the environment. This study is to summarize the bacterial species diversity, distribution in nature, their physiological characteristics, and potential biochemical pathways of those nitrogen converting microorganisms. In addition, several novel nitrogen removal technologies are also discussed for further understanding of the process optimization under both aerobic and anaerobic conditions.