Anaerobic ammonium oxidation (anammox) poses an emerging research field as it can outstand previous processes of biological wastewater treatment in terms of efficiency and costs. Anammox bacteria have the ability to metabolise NH₄⁺ and NO₂⁻ to produce N₂ under anaerobic conditions. Despite numerous studies, there is a lack of research on the co-occurrence and interrelationship of the predominant microbes that inhabit anammox-related processes. This systematic literature review follows the PSALSAR approach to assess metagenomic data on anammox bacteria and functional microbes in upstream reactors. Essential information on the physiology, metabolic pathways and inhibitory effects of anammox bacteria are reviewed and functional bacteria such as ammonia-oxidising bacteria (AOB), nitrite-oxidising bacteria (NOB), ammonia-oxidising Archaea (AOA) and denitrifying bacteria are identified. Candidatus Kuenenia and Candidatus Brocadia were the most frequently sequenced genera in the observed literature. Pseudomonadota, Chloroflexota and Bacteroidota were prevalent regardless of crucial operational parameters and configurations that affect the microbial community. Interrelationship analysis revealed a positive association between the versatility of a phylum's metabolism and its presence in the observed wastewater treatment literature. Several groups, such as Calditrichota, Myxococcota and Deinococcota are highly underrepresented, a finding that should be investigated in more detail. No evidence was found to suggest that high anammox ratios are correlated with high nitrogen removal efficiencies, as some studies found high efficiency despite low anammox abundance (<1%).