Description: Anaerobic ammonium oxidation (anammox) plays an important role in the marine nitrogen cycle. The Pearl Estuary, a typical subtropical estuary characterized by hypoxia upstream and high loads of organic matter and inorganic nutrients caused by anthropogenic activities, has received extensive attention. In this study, anammox bacterial community structures in surface sediments along the Pearl Estuary were investigated using 16S rRNA and hydrazine oxidoreductase (HZO) genes. In addition, abundance of anammox bacteria in both water and surface sediments was investigated by quantitative PCR. Obvious anammox bacterial community structure shift was observed in surface sediments, in which the dominant genus changed from “ Candidatus Brocadia” or “ Candidatus Anammoxoglobus” to “ Candidatus Scalindua” along the salinity gradient from freshwater to the open ocean based on 16S rRNA gene and HZO amino acid phylotypes. This distribution pattern was associated with salinity, temperature, pH of overlying water and particularly C/N ratio. Phylogenetic analysis unraveled a rich diversity of anammox bacteria including four novel clusters provisionally named “ Candidatus Jugangensis”, “ Candidatus Oceanicum”, “ Candidatus Anammoxidans” and “ Candidatus Aestuarianus”. The abundance of anammox bacteria in surface sediments, bottom and surface waters ranged from 4.22 × 10 5 to 2.55 × 10 6 copies g −1 , 1.24 × 10 4 to 1.01 × 10 5 copies L −1 and 8.07 × 10 3 to 8.86 × 10 5 copies L −1 , respectively. The abundance of anammox bacteria in the water column was positively correlated with NO 2 - and NO 3 - , and negatively correlated with dissolved oxygen, although an autochthonous source might contribute to the observed abundance of anammox bacteria. This article is protected by copyright. All rights reserved.