Biological nitrogen removal (BNR) is regarded as the most efficient and economically feasible method available for removal of N from municipal wastewaters.  Its use for economical treatment of animal wastewaters required development of new technologies and systems adapted to the higher-strength characteristics of these wastes and a different purpose for treatment.   Nitrification of raw flushed manure was most effective after solid-liquid separation treatment.  The discovery of a high-performing nitrifying bacterial sludge (HPNS) adapted to high ammonia concentrations (> 2500 mg N per L) and low water temperatures (5 ^oC) significantly reduced BNR plant footprint and costs.  Nitrification-denitrification with a Modified Ludzack-Ettinger (MLE) process consistently removed > 90% of the total N from swine wastewater with varying N concentrations during animal production from 660 to 2700 mg N per L .   Although anaerobic digestion is an excellent process for energy recovery from liquid manure, the digested effluent rich in ammonia is costly to treat with conventional BNR due to the low carbon remaining for denitrification. Fortunately, an autotrophic anaerobic ammonium oxidation (anammox) process is being developed that provides effective BNR to digested liquid manure.  In the anammox process the ammonia is oxidized to nitrogen gas under anaerobic conditions. Compared to conventional nitrification-denitrification, a partial nitritation-anammox mode to eliminate the ammonia from wastewater reduces 58% of the oxygen requirement and 100% of the carbon requirement. A novel anammox bacteria Brocadia caroliniensis was discovered in swine manure; it has exhibited exceptionally-high ammonia removal rates, up to 3.6 kg/cubic meter/day.  Therefore, anammox is a key technology for development of more economical and energy efficient BNR systems in the future.