A nano-sized obligate symbiont obtained from a submarine hydrothermal system north of Iceland represents a novel kingdom of Archaea—the Nanoarchaeota. Cells of Nanoarchaeum equitans are only 400 nm in diameter, resulting in a cell volume of less than 1% of an Escherichia coli cell. They grow attached to the surface of a new Ignicoccus species under strict anaerobic conditions at temperatures between 75°C and 98°C. In contrast to the Ignicoccus host cell, N. equitans possesses an S-layer. The small subunit SSU rRNA gene exhibits a unique sequence characterized by base exchanges even in segments previously thought to be identical for all organisms ("universal" signatures). N. equitans harbours a genome of only 490 kb, one of the smallest genomes known so far. The analysis of its gene content reveals only very limited biosynthetic and metabolic capacities, indicating that the symbiotic relationship to Ignicoccus is parasitic. Comparison of the membrane lipids of N. equitans and its host Ignicoccus reveals that both organisms harboured qualitatively identical lipids suggesting that the N. equitans lipids are synthesized by the Ignicoccus host. Unlike many small genome bacterial parasites, N. equitans has few pseudogenes or regions of non-coding DNA. Examination of environmental DNAs from terrestrial hot springs at Yellowstone National Park; Uzon Caldeira, Russia; and from an abyssal vent system at the East Pacific Rise resulted in the finding of further novel nanoarchaeotal SSU rRNA gene sequences, demonstrating great diversity and worldwide distribution of the Nanoarchaeota which had been completely overlooked, so far.