The complete genome of the hyperthermophilic bacterium Aquifex aeolicus has been sequenced and analyzed. This organism is one of the earliest diverging and most thermophilic bacteria known, capable of growing at temperatures up to 95°C. It uses inorganic carbon sources and is a chemolithoautotroph, relying on a complex metabolic system. Despite its small genome size (one-third that of E. coli), it exhibits metabolic flexibility. The genome contains genes for carbon fixation, biosynthesis, and oxygen respiration, and is densely packed with genes expressed in operons. The genome also includes an extrachromosomal element (ECE), which is significantly over-represented compared to the chromosome. The genome encodes enzymes for the reductive tricarboxylic acid (TCA) cycle, which is essential for carbon fixation. It also contains genes for gluconeogenesis through the Embden-Meyerhof-Parnas pathway. The organism is capable of using low levels of oxygen and has genes for oxygen respiration, suggesting that oxygen respiration was not independently evolved by the Aquifex lineage. The genome also includes genes for oxidative stress response, motility, and DNA replication and repair. The organism possesses various protective enzymes against reactive oxygen species and has genes for flagellar structure and biosynthesis. The genome of A. aeolicus is the second completely sequenced genome of a hyperthermophile. Comparative analysis with other genomes reveals differences in amino acid composition that may be related to thermostability. The phylogenetic placement of the Aquifex lineage as one of the earliest divergences in the eubacterial tree is supported by genomic data, although protein-based phylogenies do not consistently support this. The genome provides insights into the evolution of thermophilic bacteria and their metabolic adaptations. The study highlights the importance of whole-genome analysis in understanding the biology and evolution of hyperthermophiles. The genome sequence has been deposited in GenBank with accession numbers AE000657 (chromosome) and AE000667 (extrachromosomal element).The complete genome of the hyperthermophilic bacterium Aquifex aeolicus has been sequenced and analyzed. This organism is one of the earliest diverging and most thermophilic bacteria known, capable of growing at temperatures up to 95°C. It uses inorganic carbon sources and is a chemolithoautotroph, relying on a complex metabolic system. Despite its small genome size (one-third that of E. coli), it exhibits metabolic flexibility. The genome contains genes for carbon fixation, biosynthesis, and oxygen respiration, and is densely packed with genes expressed in operons. The genome also includes an extrachromosomal element (ECE), which is significantly over-represented compared to the chromosome. The genome encodes enzymes for the reductive tricarboxylic acid (TCA) cycle, which is essential for carbon fixation. It also contains genes for gluconeogenesis through the Embden-Meyerhof-Parnas pathway. The organism is capable of using low levels of oxygen and has genes for oxygen respiration, suggesting that oxygen respiration was not independently evolved by the Aquifex lineage. The genome also includes genes for oxidative stress response, motility, and DNA replication and repair. The organism possesses various protective enzymes against reactive oxygen species and has genes for flagellar structure and biosynthesis. The genome of A. aeolicus is the second completely sequenced genome of a hyperthermophile. Comparative analysis with other genomes reveals differences in amino acid composition that may be related to thermostability. The phylogenetic placement of the Aquifex lineage as one of the earliest divergences in the eubacterial tree is supported by genomic data, although protein-based phylogenies do not consistently support this. The genome provides insights into the evolution of thermophilic bacteria and their metabolic adaptations. The study highlights the importance of whole-genome analysis in understanding the biology and evolution of hyperthermophiles. The genome sequence has been deposited in GenBank with accession numbers AE000657 (chromosome) and AE000667 (extrachromosomal element).