Until now, anaerobic ammonium oxidation (anammox) has been widely applied as an alternative method to the conventional nitrification–denitrification pathway for biological nitrogen removal from wastewater. Since their discovery in a denitrifying fluidized bed reactor in the Netherlands in the early 1990s, anammox bacteria have also been detected in natural environments. Anammox is one of the newly found drivers known to contribute to the biogeochemical nitrogen cycle. In the marine environment, more than 50% of nitrogenous compounds are reportedly converted into nitrogen gas via the anammox pathway. These observations were made using state-of-the-art techniques for detecting anammox bacteria based on their lipids, small-subunit ribosomal RNA genes, functional genes, and unique reaction pathways. The research objectives for anammox bacteria are quite diverse, ranging from the application of anammox processes to various wastewater types, to anammox biochemistry and phylogeny, to elucidating how anammox bacteria have evolved. Since the genome of the anammox bacterium Kuenenia stuttgaritiensis was deciphered, anammox bacteria have proved to be quite versatile. The next challenge is to enrich knowledge of anammox bacterial physiology and phylogeny to improve their use in engineered and natural environmental systems and minimize nitrogen loads to downstream water bodies. Furthermore, rapid startup of the anammox process for engineered systems is required to broadly harness the benefits of anammox bacteria. This review article summarizes the physiology and phylogeny of anammox bacteria, detection methods of anammox bacteria and reactions, the behavior of anammox bacteria in natural environments, and recent developments in their use for engineered systems.