The three-domain system is a biological classification introduced by Carl Woese in 1990 that emphasizes his separation of prokaryotes into two groups, originally called Eubacteria and Archaebacteria. Woese argued based on differences in 16S rRNA genes that these two groups and the eukaryotes each arose separately from an ancestral progenote with poorly developed genetic machinery. To reflect these primary lines of descent, he treated each as a domain, divided into several different kingdoms. The groups were also renamed the Bacteria, Archaea, and Eukarya, further emphasizing the separate identity of the two prokaryote groups.

Although the three-domain system was quickly adopted by most molecular systematists, biologists like Luria and Mayr have criticized him for over-emphasizing the uniqueness of the archaebacteria and ignoring strong genetic similarities between the groups. Subsequent studies have confirmed that archaebacteria are unusual in the composition of their cell membrane and structure of their flagella, but are fundamentally similar to eubacteria in terms of cell structure and genetic machinery. These criticisms suggest retaining the older two-empire system (Prokaryota and Eukaryota) and using the word bacterium in its earlier meaning of prokaryote.

Which system is preferrable depends partly on the relationships of the organisms in question. Although the progenote hypothesis is discredited, molecular trees tend to group living things into the three domains, with the eukaryotes placed beside or within the Archaea and the eubacteria forming a separate branch. However, rRNA is now known to misplace some groups where it evolved rapidly (e.g. Microsporidia) and it has been argued that the root may instead belong among the eubacteria, in which case many eubacterial lines diverged before the archaebacteria did.

See also: Phylogenetic tree, Taxonomy