<P>The hyperthermophilic archaeon Thermococcus onnurineus NA1 can grow and produce H-2 on carbon monoxide (CO) and its H-2 production rates have been improved through metabolic engineering. In this study, we applied adaptive evolution to enhance H-2 productivity. After over 150 serial transfers onto CO medium, cell density, CO consumption rate and H-2 production rate increased. The underlying mechanism for those physiological changes could be explained by using multi-omics approaches including genomic, transcriptomic and epigenomic analyses. A putative transcriptional regulator was newly identified to regulate the expression levels of genes related to CO oxidation. Transcriptome analysis revealed significant changes in the transcript levels of genes belonging to the categories of transcription, translation and energy metabolism. Our study presents the first genome-scale methylation pattern of hyperthermophilic archaea. Adaptive evolution led to highly enhanced H-2 productivity at high CO flow rates using synthesis gas produced from coal gasification.</P>