ABSTRACT Here, we report the genome sequence of Bacillus subtilis strain 29R7-12, a piezophilic bacterium isolated from coal-bearing sediment down to ~2.4 km below the ocean floor in the northwestern Pacific. The strain is a Gram-positive spore-forming bacterium, closely related to Bacillus subtilis within the phylum Firmicutes . This is the first complete genome sequence of a Bacillus subtilis strain from the deep biosphere. The genome sequence will provide a valuable resource for comparative studies of microorganisms from the surface and subsurface environments.