AIMS: The aim of this study was to characterize anaerobic ammonium oxidation (anammox) community in sediments of the Dongjiang River, a drinking water source of Hong Kong. METHODS AND RESULTS: The diversity and distribution of the anammox community were investigated based on a comparative analyses of 16S rRNA and hydrazine oxidation (hzo) genes of anammox bacteria. Candidatus Brocadia and two new anammox bacterial clusters were detected based on phylogenetic analysis of 16S rRNA genes. In contrast, the targeting of hzo genes indicated the presence of only Candidatus Jettenia with four different clusters. It was found that the sequence diversities of hzo genes were higher than those of the 16S rRNA genes. The abundance of anammox bacteria varied significantly among the sediment samples based on qPCR. Pearson correlation analysis indicated that nitrite concentration was the key factor influencing the abundance of anammox bacteria. The redundance analysis (RDA) confirmed that the combination of the contents of nitrite and nitrate, and the ratio of total nitrogen vs total carbon (TN/TC) had significant impact on the anammox bacterial community structure. CONCLUSIONS: The results revealed that the diverse anammox bacteria were present in sediments of the Dongjiang River, and the community structures were associated with varied environmental factors caused by urban pollutant invasion. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report about the distribution of anammox bacterial community in sediments of the Dongjiang River, which provides helpful information of anammox niche specificity and influencing factors in the river ecosystem.