The complete genome sequence of *Aquifex aeolicus*, a hyperthermophilic bacterium, has been determined. The genome, encoding the complex metabolic machinery needed for chemolithoautotrophy, is only one-third the size of the E. coli genome. Despite its small size, *A. aeolicus* retains the ability to use oxygen as an electron acceptor, suggesting a complex respiratory apparatus. The genome contains genes for carbon fixation, biosynthesis, and respiratory processes, but lacks certain genes for anaerobic nitrate respiration. The genome is characterized by dispersed genes for biosynthetic pathways and a lack of introns or inteins. The presence of an extrachromosomal element (ECE) and the absence of homologues of key chemotaxis components suggest unique mechanisms for motility and taxis. The genome's G+C content and the presence of reverse gyrase indicate its hyperthermophilic nature. Comparative analyses with other genomes reveal trends in amino acid usage and protein stabilization strategies. The complete genome sequence provides a comprehensive resource for studying the biology and evolution of *A. aeolicus*.The complete genome sequence of *Aquifex aeolicus*, a hyperthermophilic bacterium, has been determined. The genome, encoding the complex metabolic machinery needed for chemolithoautotrophy, is only one-third the size of the E. coli genome. Despite its small size, *A. aeolicus* retains the ability to use oxygen as an electron acceptor, suggesting a complex respiratory apparatus. The genome contains genes for carbon fixation, biosynthesis, and respiratory processes, but lacks certain genes for anaerobic nitrate respiration. The genome is characterized by dispersed genes for biosynthetic pathways and a lack of introns or inteins. The presence of an extrachromosomal element (ECE) and the absence of homologues of key chemotaxis components suggest unique mechanisms for motility and taxis. The genome's G+C content and the presence of reverse gyrase indicate its hyperthermophilic nature. Comparative analyses with other genomes reveal trends in amino acid usage and protein stabilization strategies. The complete genome sequence provides a comprehensive resource for studying the biology and evolution of *A. aeolicus*.