The anammox (anaerobic ammonium oxidation) process has been used to remove nitrogen from wastewaters and is considered a promising approach due to its advantages over conventional processes (nitrification and denitrification). The development of molecular biology tools has allowed for great advances in describing the microbial communities in anammox reactors, which is important to understand the complex reactions and interactions that occur inside these systems. This study presents a review of the microbial diversity studies in anammox reactors. Several researchers have investigated the microbial community composition in anammox reactors, in order to elucidate the roles that the different microbial groups (besides the anammox bacteria) play in these systems. The microbial communities of anammox reactors appear to be affected by several factors, such as the configuration of the reactors, the biomass growth mode inside of the reactors, operational conditions and type of inoculum used for start-up. However, independent of reactors characteristics, some microbial groups such as Proteobacteria and Chloroflexi have always been found with Planctomycetes in anammox reactors. Moreover, other microbial groups such as Chlorobi, Acidobacteria and Bacteroidetes are often detected in these systems. Identifying the roles and interactions of such microorganisms inside anammox reactors is a great challenge for future studies.