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Aeropyrum pernix is a solely aerobic organism growing above 95°C under atmosphere. This marine hyperthermophilic archaeon is a member of the phylum Crenarchaeota, deeply branching within the universal phylogenetic tree based on 16S rRNA gene. It was isolated from a coastal solfataric vent in Kodakara-Jima Island in southwestern Japan and grows under strictly aerobic conditions heterotrophically on various proteinaceous complex compounds optimally at 90 to 95°C. The other closely related species in the genus, Aeropyrum camini, was isolated from a deep-sea hydrothermal vent at the Suiyo-Seamount in the Izu-Bonin Arc, Japan, at a depth of 1385 m. The cell membrane of A. pernix is mainly composed of unique polar lipids. The complete genome sequence of A. pernix K1 has been determined for the first time in Crenarchaeota. Three introns are surprisingly located within the rRNA operon, two of which harbor homing endonucleases. Two proviral regions were identified in the genome and they were practically induced under suboptimal condition. Another two novel viruses are also isolated from the geothermal environment. Due to its unique phenotypes (aerobic and hyperthermophilic), a lot of enzymes from A. pernix are studied for industrial applications. Extracellular and intracellular proteases, SOD and hydrogenase showed oxygen tolerance and high thermo stability above 100°C, meaning that they can be practically applied as industrial catalysts. Further, a cysteine synthase with an extremely high activity, which catalyzes the formation of L-cysteine, has been applied to produce L-cysteine used as materials for medicines and cosmetics for whitening effects. This archaeon has extreme potential in industry.