Anaerobic ammonium oxidation (anammox) widely occurs in marine ecosystems, and it plays an important role in the global nitrogen cycle. But in freshwater ecosystems its occurrence, distribution and contribution, especially in extreme environments, are still not well known. In this study, anammox process was investigated in some extreme environments of freshwater ecosystems, such as those with high (above 75°C) and low (below −35°C) temperature, high (pH > 8) and low (pH < 4) pH and eutrophy (the concentration of NH4+-N > 300 mg kg−1). The polymerase chain reaction (PCR) screening results showed that anammox bacteria were widespread in the examined sediments from freshwater extreme environments. Quantitative PCR showed that the abundance of anammox bacteria ranged from 6.94 × 104 to 8.05 × 106 hydrazine synthase (hzsB) gene copies g−1 dry soil. 15N-labelled incubation experiments indicated the occurrence of anammox in all examined sediments and the potential anammox rates ranged from 0.02 to 6.24 nmol N g−1 h−1, with a contribution of 3.45–58.74% of the total N2 production. In summary, these results demonstrate the occurrence of anammox in these extreme environments, inferring that anammox may harbour a wide ecological niche in the freshwater ecosystems.