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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 that, based on differences in 16S rRNA genes, 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.

A phylogenetic tree based on rRNA data, showing the separation of bacteria, archaea, and eukaryotes.

Although the three-domain system was quickly adopted by most molecular systematists, biologists like Ernst Mayr criticized him for over-emphasizing the uniqueness of the archaebacteria and ignoring strong genetic similarities between the groups. Subsequent studies have confirmed that the archaea are unusual in the composition of their cell membrane and structure of their flagella. Other significant differences include archaeal systems for DNA replication and transcription which bear distinct similarity to those found in eukaryotes. For instance, archaeal RNA polymerase consists of up to 14 subunits, whereas most bacterial RNA polymerases have only 4 subunits. Analysis of these subunits suggests that they are more closely related to those found in eukaryotes. Also, the archaea produce a number of DNA-binding proteins with similarity to eukaryotic histones.

Nevertheless, a minority viewpoint suggests retaining the older two-empire system (Prokaryota and Eukaryota) and using the word bacterium in its earlier meaning of prokaryote.

Which system is preferable 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, it has been suggested this is an artifact of long branch attraction and that the root may instead belong among the eubacteria, in which case many eubacterial lines diverged before the archaebacteria did.

In 2006, the discovery of unique properties of the Mimivirus started a discussion about classification of (certain) viruses as a fourth domain of life.

• Phylogenetic tree
• Taxonomy
• Two-empire system
• Five-kingdom system