The global nitrogen biogeochemical cycling processes are predominantly driven by bacteria including: N2 fixation, nitrification, denitrification, ammonification, and a new process, anaerobic ammonia oxidation (Anammox), which is a more recently described bacterial contribution to the nitrogen cycle. With the development and application of metagenomics and other molecular approaches, new “players” in the nitrogen cycle-ammonia oxidizing archaea (AOA) have also been identified. Our understanding of nitrogen cycling processes and the microorganisms that mediate them has been greatly improved with these two major breakthroughs in recent years. This review summarized some major advances in the microbial ecology of anaerobic, archaeal, and bacterial ammonia oxidisers.