Hydrogenobacter thermophilus is a chemolithoautotroph that utilizes not only hydrogen (H(2)) but also thiosulfate as sole source of energy and assimilates carbon dioxide via the reductive tricarboxylic acid (RTCA) cycle. We systematically carried out transcriptome analysis of metabolic enzymes in both H(2)- and thiosulfate-grown H. thermophilus cells. The analysis indicated that the expression of hydrogenase genes is repressed under thiosulfate oxidation conditions as compared with H(2) oxidation conditions. This was confirmed by enzyme assay. In contrast, some genes for sulfur metabolism, including sox genes, showed almost the same expression levels under both conditions. In addition, the genes for the RTCA cycle showed high expression levels under both conditions. It was suggested that sulfur metabolism and the RTCA cycle function as forms of basal metabolism, and H(2) oxidation is inducible. Switching of H(2) oxidation can be advantageous for the lifestyle of this bacterium in nature.