Wetlands are one of the most important ecosystems on Earth, providing highly valued ecosystem services. They contribute to flood control, shoreline stabilization, regulate climate, and mitigate climate change by capturing and storing carbon. Wetlands are sinks of greenhouse gasses (GHG) but are also a natural source of atmospheric GHG emissions. The three major GHG are carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). Emission rates of GHG depend on the way they are produced in ecosystems and how long they remain in the atmosphere. Production and consumption of GHG in wetlands are enhanced by microorganisms involved in the C and N cycle. In this study, we estimated GHG from wetlands soils along a natural gradient from fringe mangroves (FM), saltmarsh (SM), basin mangrove (BM), to floodplain tree swamps (floodplain). We characterized the diversity of microbial community and measured physicochemical variables in situ. To estimate the contribution of natural wetlands to the global GHG emissions, to identify microbial community and potential environmental parameters associated with GHG. We found that GHG emissions from natural wetlands soils are negligible compared to emissions from other land-use ecosystems. The highest CH4 emission found in our study was from the floodplain, followed by FM, BM, and SM (1.76±1.66, 1.14±0.10, 0.05±0.03, 0.05±0.04 gr CH4 m-2 yr-1, respectively). Alphaproteobacteria and Gammaproteobacteria were the most dominant bacteria in all wetlands, followed by Planctomycetes, which was more dominant in the floodplain. Members of Desulfobacterota were present in both FM and BM. In the floodplain, Verrumicrobia was a dominant group. Regarding archaea, Halobacteria showed a decrease from FM to the floodplain. While Micrarchaeota and Thermoplasmatota showed an increase from FM to the floodplain. Our results can be used as a reference for emerging projects on restoration, and protection of natural wetlands for climate change, nutrient offsets, and biodiversity credit mechanisms.