[Objective] Recently, as the prevalence of multiple antibiotic resistant bacteria in environments are induced by the extensive use of antibiotics by human, a better understanding of the distribution, transport and dissemination of antibiotic resistance genes (ARGs) in environments is warranted. The objective of this study was to determine the pollution levels of antibiotic resistance genes in Jiulong River estuary and wastewater treatment plants (WWTPs) in Xiamen. [Methods] Polymerase chain reaction (PCR) assays were employed to identify the distribution patterns of four sulfonamide, thirteen tetracycline ARGs and two integron genes in water, sediments of Jiulong River estuary and five activated sludges in WWTPs of Xiamen. Clone libraries of the tet(W) gene were also generated from three sediments of Jiulong River estuary and five WWTPs in Xiamen. [Results] The all ARGs has been dectected except tet(O) and tet(S). The results demonstrated that the frequency of detection (FOD) of ARGs and integron genes in environmental samples with the highest FOD in activated sludges (0.86), moderate FOD in sediments (0.57) and the lowest FOD in water (0.24). Furthermore, the FODs of sul(l), int(1), tet(A), tet(C), tet(E), tet(M) and tet(W) were higher in freshwater and brackish water than those in seawater, suggesting that ARGs may be transported from the upstream of Jiulong River. [Conclusion] Principle component analysis also supported the suggestions that WWTPs contained the highest ARGs, and ARGs are enriched in sediments but unstable in water. In addition, the results of tet(W) libraries indicated that WWTPs may be a point source of ARGs into Jiulong River estuary and Xiamen sea.