Abstract:[Objective] Coastal wetland ecosystems, situated at the interface of freshwater and seawater, are characterized by the seepage of groundwater with high Fe2+ concentrations into the surface layers of sediments, which forms wetland runoff. This runoff, combined with periodic tidal flooding, creates an oxic-anoxic interface conducive to the bio-oxidation of Fe2+ by Fe-oxidizing bacteria. However, there is a lack of comprehensive assessment of Fe-oxidizing bacterial communities in coastal wetland ecosystems. [Methods] We measured the basic environmental parameters such as the oxygen penetration depth in the sediments of five coastal wetland sites in Xisha Wetland Park in Chongming, Shanghai and Dongsha Beach in Zhujiajian Island in Zhoushan, Zhejiang. The community composition and distribution of bacteria and Fe-oxidizing bacteria were comprehensively deciphered by 16S rRNA gene amplicon sequencing. [Results] Dongsha Beach in Zhujiajian Island exhibited deeper oxygen penetration (reaching more than 10 mm) than Xisha Wetland in Chongming. The non-metric multidimensional scaling (NMDS) results indicated that the bacterial community structure was primarily influenced by environmental conditions that varied with geographical location, while the community structure of Fe-oxidizing bacteria was influenced by both the geographical location of the sampling sites and the oxygen penetration depth of the sediments. The dominant bacteria in Xisha Wetland and Dongsha Beach were Cyanobacteria, Gammaproteobacteria, Bacteroidetes, Alphaproteobacteria, and Actinobacteria. The dominant genera of Fe-oxidizing bacteria were Gallionella, Rhodobacter, Lepthothrix, and Sideroxydans. [Conclusion] We studied the Fe-oxidizing bacteria in the sediments of Xisha Wetland in Chongming and Dongsha Beach in Zhujiajian Island and discovered that the composition of Fe-oxidizing bacterial communities was closely linked to the oxygen penetration depth variations caused by different types of wetland sediments.