Anaerobic ammonium oxidation (anammox) and nitrite-dependent anaerobic methane oxidation (n-damo) processes are two newly discovered biochemical pathways for removal of reactive nitrogen species and methane. An investigation was initiated to investigate the simultaneous removal of ammonium and methane and the corresponding microorganisms in a full-scale sewage treatment plant and four landfill leachate treatment plants. In this study, hzsB and pmoA genes were used to amplify the genomic DNA of these samples to reveal the diversity of anammox bacteria and n-damo bacteria in these WWTPs. Both anammox bacteria and n-damo bacteria were detected successfully in all samples. The hzsB gene-based PCR amplified sequences featured three genera of Candidatus (Ca.) Brocadia, Ca. Kuenenia and Ca. Jettenia in these WWTPs, while the pmoA gene amplification showed two species of Ca. Methylomirabilis oxyfera and Ca. Methylomirabilis sinica. It was observed that after inoculation of anammox sludge, Brocadia becomes more dominant from the initial co-existing consortium of Kuenenia and Brocadia, and the community diversity decreased accordingly. Based on quantitative 16S rRNA gene PCR, the abundance of anammox bacteria ranged from 2.64 × 106 to 1.73 × 1013 copies per gram dry sludge in the five plants, particularly high on the carriers of landfill leachate wastewaters and the abundance of n-damo bacteria ranged from 2.52 × 107 to 2.19 × 108 copies per gram dry sludge in the five plants. Results shows that abundances of anammox bacteria and AOB (ammonium oxidizing bacteria) were limited by the lower ammonium in the sewage treatment plant, but were higher corresponding to ammonium concentration. Successful inoculation of anammox bacteria was achieved in practical engineering systems and the co-occurrence of anammox bacteria and n-damo bacteria plays an important role in N and C removal in WWTPs. •Both anammox and n-namo bacteria are detected in wastewater treatment plants.•Abundance of n-damo is several order of magnitude lower than that of anammox bacteria.•Much high abundance and affinity of anammox bacteria to surfaces are evident.•Wastewater treat can take advantage of them save energy and decrease emission of greenhouse gas.