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Many cities are located in the downstream areas of rivers. Rapid urbanization may result in drastic changes in the urban river ecosystem. Antibiotic resistant genes (ARGs) are considered to be emerging environmental pollutants, which may do harm to the health of humans and may pose a potential risk for urban ecological safety by the dissemination and enrichment of ARGs in urban rivers. In this study, a high-throughput quantitative PCR technique was used to investigate the diversity and abundance of ARGs at three sites in Lianjiang County and the estuary of the Aojiang River, Fujian Province. The results show the abundance of ARGs in the downstream urban area of Lianjiang County (3.9×10 10 copies·L -1 ) is significantly higher than upstream of the urban area and the estuary of the Aojiang River. A total of 129 ARGs are detected in the downstream urban area, which is higher than in the upstream and the estuary. The results also suggest that ARGs are persistent and not easy to reduce in the natural river following the occurrence of ARGs and indicated that the urban river is an important reservoir of ARGs.