Modern hydrothermal Fe-Si oxyhydroxide deposits are now known to be analogues to ancient siliceous iron formations. In this study, samples of Fe-Si oxyhydroxide deposits were collected from hydrothermal field on the Southwest Indian Ridge. An investigation of mineralization in these deposits was carried out based on a series of mineralogical and morphological methods. X-ray diffraction and selected area electron diffraction analysis show that amorphous opal and poorly crystalline ferrihydrite are the major minerals. Furthermore, some typical filament structures detected by scanning electronic microscopy examinations, probably indicating the presence of Fe-oxidizing bacteria (FeOB), are pervasive with the main constituents being Fe, Si, P, and C. We thus believe that chemolithoautotrophic FeOB play a significant role in the formation of Fe oxyhydroxide which can effectively oxidize reduced Fe(II) sourced from hydrothermal fluids. Precipitation of amorphous silica, in contrast, is only a passive process with the Fe oxyhydroxide acting as a template. The distinct microlaminae structure alternating between the Fe-rich and Si-rich bands was observed in our samples for the first time in modern seafloor hydrothermal systems. We propose that its formation was due to the episodic temperature variation of the hydrothermal fluid which controls the biogenic Fe oxyhydroxide formation and passive precipitation of silica in this system. Our results might provide a clue for the formation mechanism of ancient banded iron formations.