Methane gas (CH 4 ) reservoirs have previously been reported in tropical marine sediments of Saco do Mamanguá ria (Rio de Janeiro, Brazil). It is known that a methane microbiome can be established in methane seeps sites; however, they are still poor investigate the spatial and vertical distribution of the bacterial and archaeal composition and the community structure in the sediments of Saco do Mamanguá ria. For this purpose, we collected sediment samples through 100 cm long gravity corer at

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... ee different sites and performed community analysis based on 16S rRNA gene sequencing, quantification of the methyl coenzyme M reductase-encoding gene (mcrA) and geochemical analysis, including CH 4 stable isotope. Our results revealed a biogenic trend for CH 4 isotopic signature and a high proportion of archaeal sequences assigned as Bathyarchaeota, with a spatial distribution throughout the inner areas of the channel and the deepest strata. OTUs classified within Bathyarchaeota and Chloroflexi (Dehalococcoidia) showed positive correlation with methane concentrations, sediment depth and oxidation-reduction potential. Due to their prevalence in the microbial community, we also performed phylogenetic analysis to understand the closeness of our Bathyarchaeota OTUs with Bathyarchaeota subgroups, and the results demonstrated a close relationship particularly with Bathy-8 and Bathy-13, which possess genes for acetogenesis and methanogenesis. Although direct relations between microbial populations and the biogenic methane emissions in Saco do Mamanguá cannot be assured, our results emphasize the importance of further investigations about the potential role of Bathyarchaeota in the carbon cycling in methane-rich tropical shallow ecosystems.