Recirculation aquaculture systems (RASs) are increasingly considered as production systems of the future with a minimum ecological impact for the production of aquatic food. To maintain a good water quality and to produce quality and healthy fishery products, the systems depend on a diverse microbial community involved in different processes of water purification but also in unwanted effects. The article reviews the present knowledge on microorganisms in RAS, their relative distribution within the system compartments and their role in system performance. The system possesses different microniches in which microorganisms retrieve their preferential conditions for oxygen and nutrients. Ammonia and nitrite are oxidized under aerobic conditions into less toxic compounds. Anaerobic ammonium oxidizers in the biofilm oxidize anaerobically both ammonia and nitrites into less harmful dinitrogen gas. Heterotrophic bacteria mineralize organic matter derived from uneaten feeds, dead bodies and excreta of fish. Under conditions of high organic load and high C/N content, nitrifiers are overgrown by heterotrophs with negative effects to the nitrification process. For not yet understood reasons, the presence of off-flavour-producing microorganisms occurs also in RAS. Microbial management and management of inputs to the systems to prevent the proliferation of pathogens are discussed and possible management techniques of off-flavours are also presented. Research orientations are given to explore further the potential of heterotrophic bacteria in microbial management and intensive aquaculture production in systems other than RAS.