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[1] We examined two low-temperature hydrothermal deposits rich in Fe-Si-Mn collected from the recently discovered hydrothermal fields at the Southwest Indian Ridge using mineralogical, geochemical, and molecular biological techniques. The mineralogical and geochemical analyses indicated that the low-temperature hydrothermal fields would provide a warm and chemical species-rich habitat for chemosynthetic-based hydrothermal ecosystems. Analyses of 16S rRNA sequences showed that z-Proteobacteria, Pseudoalteromonas, Leptothrix, and Pseudomonas were potential Fe and Mn oxidizers in the low-temperature hydrothermal environments, but they were not present in equal abundance among the subniches. Some potential Fe and Mn reducers were also recovered; they were more commonly found in the exterior black Fe-Mn oxides. The difference between the exterior black Fe-Mn oxides and the interior Opal-A could be related to differences in in situ physicochemical conditions. We also identified microbial players that may participate in sulfur (S) geochemical cycling in these low-temperature hydrothermal environments via analyses of 16S rRNA sequences and the aprA functional gene. The results indicated that members of g-Proteobacteria and a-Proteobacteria were involved in the S oxidation process, while members of d-Proteobacteria, Nitrospirae, Firmicutes, and Archaea might participate in the S reduction process. Fe, Mn, and S oxidizers and reducers might actively participate in hydrothermal biogeochemical processes, which could influence the transfer of chemical species and the formation of biogenic minerals.