Abstract: Urban rivers represent a unique ecosystem in which anthropic intervention occurs regularly. However, the spatial distribution of ammoniaoxidizing bacteria (AOB) and ammoniaoxidizing archaea (AOA) in the urban river has not well documented. Here, a comprehensive analysis of AOA and AOB in the surface water and sediments in Nanchong section of Jialing River and its two urban branches was conducted using 16S rRNA genebased Illumina MiSeq sequencing. Results were as follows: (1) The total phosphorus and inorganic nitrogen of urban branch were significantly higher than those in main Jialing River. (2) Realtime quantitative PCR of ammonia monooxygenase (amoA) genes showed that the ratios of AOA/AOB were 086-631 and 179-6985 in surface water and sediment, respectively, which indicating AOA mostly predominated over AOB. But the abundance of AOB in urban branches was much higher than that of AOA. (3) AOB in surface water and sediment in Jialing River were mostly affiliated to Nitrosococcus oceanilike lineage，while the dominant AOB in urban branches and drain outlet fell within Nitrosococcus oceanilike lineage. (4) Redundancy analysis suggested that NH4+-N content in surface water was the most significant driver determining the AOB community composition in the Jialing River. (5) The AOA community in Jialing River was dominanted by Candidatus Nitrosoarchaeum and Nitrososphaera, the latter was highly enriched in urban branches. Findings highlight that ammonia oxidizers exhibit spatial variations in Jialing River (Nanchong section) and urban branches. The joint influence of sewage discharging and contaminated urban branches could be the main factors to sharp the community of ammoniaoxidizing microorganisms.