Hydrogenobacter thermophilus is a thermophilic, obligately chemolithoautotrophic and aerobic hydrogen-oxidizing bacterium. It is unique in its ability to fix carbon dioxide via the reductive tricarboxylic acid cycle under aerobic conditions. It utilizes molecular hydrogen, elemental sulfur, or thiosulfate as the sole energy source. Here, we report the complete genome sequence of H. thermophilus TK-6.