Deep-sea sediments can reveal much about the last 200 million years of Earth history, including the history of ocean life and climate. Microbial diversity in Afanasy Nikitin seamount located at Equatorial East Indian Ocean (EEIO) was investigated. Deep sea sediment collected at 150 cm depth (~67 ky BP) exhibited a dominance of clones clustering in the phylum Firmicutes (63%), followed by γ-Proteobacteria (37%). The bacterial diversity within sediment at 200 cm depth (∼84 ky BP) was dominated by γ-Proteobacteria (66%) followed by β- Proteobacteria (34%), whereas no Firmicutes clones were retrieved. Notably, 29% clones from 150 cm and 18% of clones from 200 cm sediment showed high identity to sequences previously reported from mining sites, while 21% of clones from 150 cm depth and 10% from 200 cm sediments showed identity to sequences previously reported from volcanic areas. Further, many of the sequences were from uncultured clones. Overall, these data may help elucidate the nature of microorganisms inhabiting these sites and unravel the molecular diversity of the deep sea from an evolutionary perspective.