Display omitted •A total nitrogen removal rate of 0.18gNg−1VSSd−1 was obtained in the reactor.•Flexible flocs and compact granules were both found in the system.•Proteobacteria, Chloroflexi and Planctomycetes were selected over the startup.•Filamentous bacteria constitute a large portion (>25%) in the reactor. The combined nitritation–anammox process has recently been studied extensively from an engineering perspective. However, the importance of microbial communities of this process was generally underestimated. In this study, a lab-scale nitritation–anammox sequencing batch reactor (SBR) was established and the microbial community structure was further characterized, in order to provide the comprehensive insight into the key microbial groups in one-stage nitritation–anammox system. In general, a total nitrogen removal rate of 0.18gNg−1VSSd−1 was obtained after 180days when the nitrogen loading rate was 0.5kgNm−3d−1 (hydraulic retention time of 1d). Flexible flocs and compact granules were both found in the system, and this morphological differences were basically caused by the different microbial compositions, that is, flocs mainly consisted of filamentous bacteria and granules dominated by anammox bacteria. Results from high-throughput sequencing analysis revealed that Proteobacteria, Chloroflexi and Planctomycetes were selected and established a stable foothold in the community over the startup period, probably driven by the availability of substrate in the influent. Apart from nitrifiers of the Proteobacteria and anammox bacteria of the Planctomycetes, members of Chloroflexi constitute a large portion (>25%), which indicate that heterotrophs (Chloroflexi) survived by soluble microbial products (SMP) of autotrophs should not be neglected in the autotrophic system. This study could be useful for better understanding of one-stage nitritation–anammox system, especially for the interaction between autotrophs and heterotrophs in the system.