The three-domain system recognizes bacteria, archaea and eukaryotes as three domains. In 1990, Woese, Kandler and Wheelis proposed the domain rank and the names Bacteria, Archaea and Eucarya, using molecular comparisons to argue that the older prokaryote/eukaryote division hid important differences. See Woese, Kandler and Wheelis, 1990: Towards a natural system of organisms.
The associated three-domain ancestry model places the nuclear lineage of eukaryotes alongside archaea, rather than within them. This historically influential interpretation should be distinguished from the two-domain system; listing three familiar groups does not establish three independent primary branches.
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