With the development of the aquaculture industry for high efficiency, energy saving, and environmentally friendly methods, recirculating aquaculture has attracted increasing attention from researchers and practitioners. A recirculating aquaculture system (RAS) consists primarily of an aquaculture module and a water purification module. In the aquaculture module, nitrogen in the feed could be released into the water phase through various routes (i.e., the feedstuff residue and aquaculture animal excretion), whose species can be transformed by microbes. Free ammonia and nitrite have acute toxic effects on aquaculture animals, rendering the efficient removal of ammonia and nitrite essential for the RAS. Compared with physical and chemical methods, biological treatment methods based on microbial nitrification can convert ammonia and nitrite into less toxic nitrate with the advantages of good treatment performance, low operation cost, and little secondary contamination, and have been widely utilized in the purification of multiple wastewaters (e.g., municipal wastewater, industrial wastewater, agricultural wastewater, and ammonia-contaminated groundwater). For the treatment of recirculating water with low and fluctuating nitrogen loads, a biofilm process based on the attached growth of microbes is more suitable than an activated sludge process based on the suspended growth of microbes. To date, a variety of biofilm processes have been developed, among which the fixed-bed biofilm reactor (FBBR) and moving-bed biofilm reactor (MBBR) have been widely investigated for the control of ammonia and nitrite in aquaculture wastewater. However, the relevant studies were mostly conducted in laboratory- and pilot-scale RASs. Thus, there is still a lack of comparative investigations of FBBR and MBBR, which are simultaneously operated in a full-scale RAS.Therefore, a parallel FBBR and MBBR were joined to a full-scale RAS for Macculochella peeli. The FBBR and MBBR were simultaneously and continuously operated for 35 d to investigate variations in their water quality and microbial community structures. The results indicate that the FBBR and MBBR had similar variations in ammonia, nitrite, nitrate, and pH in the effluents. Over the entire operational period, the dissolved inorganic nitrogen (DIN) concentrations gradually increased; the ammonia and nitrite concentrations and their proportions in DIN first increased and then decreased stepwise; and the nitrate concentrations increased gradually, while the variation in the nitrate proportions in DIN was opposite to that of ammonia and nitrite. Both the FBBR and MBBR could transform ammonia and nitrite to nitrate, which resulted in nitrate accumulation and a pH decrease in aquaculture water. During the operation period, the nitrification capacity gradually matured, and ammonia oxidation could occur prior to nitrite oxidation. At 35 d, the concentrations of ammonia, nitrite and nitrate were 0.32 (0.29), 0.27 (0.22) and 29.75 (29.76) mg/L with their proportions in DIN of 1.05% (0.96%), 0.90% (0.72%) and 98.05% (98.32%) in FBBR (MBBR) effluent; pH declined from7.62 (7.59) to 7.25 (7.22) in FBBR (MBBR) effluent.The number of operational taxonomic units (OTU) obtained from the FBBR and MBBR samples were 2, 088 and 1, 852, respectively, and 1, 174 OTUs were shared between FBBR and MBBR. The α indices (Chao1, ACE, Shannon, and Simpson) from the biofilm reactors indicated that FBBR possessed higher richness and diversity of the microbial community than MBBR, which could be attributed to the difference in the internal environment between FBBR and MBBR. In total, 16 phyla, 28 classes, and 149 genera were identified in the FBBR samples, which were slightly fewer than those from the MBBR samples (i.e., 19 phyla, 31 classes, and 155 genera). However, the relative abundance of microbes demonstrated that FBBR and MBBR had similar predominant microbes: Proteobacteria (69.42% in FBBR and 86.92% in MBBR) at the phylum level, γ-Proteobacteria (40.71% in FBBR and 64.36% in MBBR) and α-Proteobacteria (26.58% in FBBR and 21.74% in MBBR) at the class level, and Acinetobacter (27.50% in FBBR and 53.29% in MBBR) at the genus level. Nitrosomonas and Nitrospira constituted the nitrifiers in both FBBR and MBBR, but the relative abundance of nitrifiers was higher in FBBR. Furthermore, the relative abundance of Nitrospira was far higher than that of Nitrosomonas, indicating that complete ammonia oxidation bacteria might exist in FBBR and MBBR. In addition, Vibrio was not found in FBBR and MBBR, but Bdellovibrio was observed. The results of this study can provide technical support for the selection of biological purification technology for RAS, and thus improve the green development of the aquaculture industry.Future studies will focus on: Investigating the effects of water quality conditions and operational parameters on the water treatment performance of FBBR and MBBR; Determining the species of complete ammonia oxidation bacteria and their relative abundances on the filler surface in FBBR and MBBR; Effectively eliminating nitrate in the aquaculture water by introducing microbial denitrification process after FBBR and MBBR to control the total nitrogen in RAS; Establishing a flexible and feasible strategy for controlling the pH in recirculating water by exploring the solid-phase buffers that could serve as the slow-release sources of alkalinity in the biofilm reactor.