Anaerobic ammonium oxidation (anammox) is a microbial process in which NH4+ is oxidized to N2 gas with NO2− as an electron acceptor. The anammox process is mediated by bacterial members affiliated with the phylumPlanctomycetes, which are ubiquitously detected from anoxic natural and man-made ecosystems and a key player in the global nitrogen cycle. In the past two decades, phylogenetically different anammox bacteria have been recognized in natural and synthetic ecosystems (i.e. ‘CandidatusKuenenia’, ‘Candidatus Brocadia’, ‘CandidatusJettenia’, ‘CandidatusAnammoxoglobus’ and ‘CandidatusScalindua’ genera), and the geographic distributions of these anammox bacteria indicate that they have genus-specific or species-specific habitats. Recently, we revealed the physiological characteristics of ‘Ca. Jettenia’ in addition to ‘Ca. Kuenenia’, ‘Ca. Brocadia’ and ‘Ca. Scalindua’, and, as a result, it is possible to compare the physiological characteristics of the anammox bacteria and discuss their niche partitioning. Therefore, we summarize the current knowledge of anammox bacterial ecology and physiology in this review to assess the potential ecological niche partitioning of anammox bacteria in natural and synthetic ecosystems.