The newly recognized ammonia-oxidizing archaea (AOA) makes re-evaluation of the contribution to ammonia oxidization by both AOA and ammonia-oxidizing bacteria (AOB) necessary and meaningful. The growing population and increasing anthropogenic activities around coastlines have affected wetland and coastal marine ecosystems through discharging polluted water containing large amounts of reactive inorganic nitrogen. The objectives of this study were to detect the phylogenetic diversity and abundance of ammonia oxidizers including AOA and AOB on different scales and to elucidate the distribution patterns along an anthropogenic pollution gradient from the coastal wetland of the Mai Po Nature Reserve in Hong Kong to the South China Sea (SCS). Generally, besides lineages shared by similar environments, various endemic lineages were also observed in the polluted mangrove sediments of Hong Kong, and in the coastal, and deep-sea surface and subsurface sediments from the SCS indicating their geographical distance should be responsible for these phylogenetic distinctions. The community structures of AOA and AOB observed were proposed to be associated with environmental parameters including metals and total phosphorus (TP) separately in the sediments while their abundance was correlated with the pH value and temperature. On the other hand, along a profile of surface sediments with stable salinity from the coastal margin to the slope in the SCS, a clear community structure transition was detected for both AOA and AOB, showing major differences in each of their responses. Although the abundance of AOA was lower than that of AOB in the subsurface sediment samples from the SCS, the statistical support for relationships between AOA and nitrite concentration shed new light on the active contributor to the subsurface nitrogen cycle in the oxygen minimum zone from the deep-sea sediments. On a large scale, along the anthropogenic pollution gradient from the Pearl River Delta to the coastal margin and then the SCS, the dominant genus ...