A novel thermophilic chemotrophic bacterium, strain SS56^T, was isolated from Nakabusa Hot Spring, Japan. The isolate was a rod-shaped (1.5–2.1×0.6–0.8 µm), Gram-stain-negative bacterium. The cells of this strain grew chemoheterotrophically under aerobic and anaerobic conditions. Autotrophic growth was observed with thiosulphate and elemental sulphur under aerobic conditions but not with H₂ as the electron donor. Heterotrophic growth in the presence of O₂ occurred on yeast extract, tryptone, polypeptone and organic acids. Strain SS56^T used nitrite as an alternative electron acceptor under anaerobic chemoheterotrophic conditions. The isolate grew between 35 and 65 °C, with the optimum at 55 °C. The pH range for growth was pH 6.0–9.0; optimal growth occurred at pH 7.0–8.0. The 16S rRNA gene sequence of strain SS56^T was 98.9% identical to that of Hydrogenophilus thermoluteolus TH-1^T. The draft genome sequence of 2401804 bp for strain SS56^T gave values of 53.7% for digital DNA–DNA hybridization, 92.9% for average nucleotide identity and 93.6% for average amino acid identity compared with the genome sequence of 2223143 bp for H. thermoluteolus TH-1^T. Based on the information described above, strain SS56^T (=DSM 111892^T=JCM 34254^T) is proposed as the type strain of a novel species, Hydrogenophilus thiooxidans sp. nov.