Three Domain System

Three Domains of Life

Tree of Life
Organisms are classified into three Domains: Bacteria, Archaea, and Eukaryota. Public Domain

The Three Domain System, developed by Carl Woese, is a system for classifying biological organisms. Over the years, scientists have developed several systems for the classification of organisms. From the late 1960's, organisms had been classified according to a Five Kingdom system. This classification system model was based on principles developed by Swedish scientist Carolus Linnaeus, whose hierarchical system groups organisms based on common physical characteristics.

The Three Domain System

As scientists learn more about organisms, classification systems change. Genetic sequencing has given researchers a whole new way of analyzing relationships between organisms. The current system, the Three Domain System, groups organisms primarily based on differences in ribosomal RNA (rRNA) structure. Ribosomal RNA is a molecular building block for ribosomes.

Under this system, organisms are classified into three domains and six kingdoms. The domains are Archaea, Bacteria, and Eukarya. The kingdoms are Archaebacteria (ancient bacteria), Eubacteria (true bacteria), Protista, Fungi, Plantae, and Animalia.

Archaea Domain

This domain contains single-celled organisms known as archaea. Archaea have genes that are similar to both bacteria and eukaryotes. Because they are very similar to bacteria in appearance, they were originally mistaken for bacteria. Like bacteria, Archaea are prokaryotic organisms and do not have a membrane bound nucleus.

They also lack internal cell organelles and many are about the same size as and similar in shape to bacteria. Archaea reproduce by binary fission, have one circular chromosome, and use flagella to move around in their environment as do bacteria.

Archaea differ from bacteria in cell wall composition and differ from both bacteria and eukaryotes in membrane composition and rRNA type.

These differences are substantial enough to warrant that archaea have a separate domain. Archaea are extreme organisms that live under some of the most extreme environmental conditions. This includes within hydrothermal vents, acidic springs, and under Arctic ice. Archaea are divided into three main phyla: Crenarchaeota, Euryarchaeota, and Korarchaeota. ​

  • Crenarchaeota include many organisms that are hyperthermophiles and thermoacidophiles. These archaea thrive in environments with great temperature extremes (hyperthermophiles) and in extremely hot and acidic environments (thermoacidophiles).
  • Archaea known as methanogens are of the Euryarchaeota phylum. They produce methane as a byproduct of metabolism and require an oxygen-free environment.
  • Little is known about Korarchaeota archaea as few species have been found living in places such as hot springs, hydrothermal vents, and obsidian pools.

Bacteria Domain

Bacteria are classified under the Bacteria Domain. These organisms are generally feared because some are pathogenic and capable of causing disease. However, bacteria are essential to life as some are part of the human microbiota. These bacteria preform vital functions, such as enabling us to properly digest and absorb nutrients from the foods we eat.

Bacteria that live on the skin prevent pathogenic microbes from colonizing the area and also aid in the activation of the immune system. Bacteria are also important for the recycling of nutrients in the global ecosystem as they are primary decomposers.

Bacteria have a unique cell wall composition and rRNA type. They are grouped into five main categories:

  • Proteobacteria: This phylum contains the largest group of bacteria and includes E.coli, Salmonella, Heliobacter pylori, and Vibrio. bacteria.
  • Cyanobacteria: These bacteria are capable of photosynthesis. They are also known as blue-green algae because of their color.
  • Firmicutes: These gram-positive bacteria include Clostridium, Bacillus, and mycoplasmas (bacteria without cell walls).
  • Chlamydiae: These parasitic bacteria reproduce inside their host's cells. Organisms include Chlamydia trachomatis (causes chlamydia STD) and Chlamydophila pneumoniae (causes pneumonia).
  • Spirochetes: These corkscrew-shaped bacteria exhibit a unique twisting motion. Examples include Borrelia burgdorferi (cause Lyme disease) and Treponema pallidum (cause syphilis).

Eukarya Domain

The Eukarya domain includes eukaryotes, or organisms that have a membrane bound nucleus. This domain is further subdivided into the kingdoms Protista, Fungi, Plantae, and Animalia. Eukaryotes have rRNA that is distinct from bacteria and archaeans. Plant and fungi organisms contain cell walls that are different in composition than bacteria. Eukaryotic cells are typically resistant to antibacterial antibiotics. Organisms in this domain include protists, fungi, plants, and animals. Examples include algae, amoeba, fungi, molds, yeast, ferns, mosses, flowering plants, sponges, insects, and mammals.

Comparison of Classification Systems

Five Kingdom System


Three Domain System
Archaea DomainBacteria DomainEukarya Domain
Archaebacteria KingdomEubacteria KingdomProtista Kingdom
  Fungi Kingdom
  Plantae Kingdom
  Animalia Kingdom


As we have seen, systems for classifying organisms change with new discoveries made over time. The earliest systems recognized only two kingdoms (plant and animal). The current Three Domain System is the best organizational system we have now, but as new information is gained, a different system for classifying organisms may later be developed.

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Your Citation
Bailey, Regina. "Three Domain System." ThoughtCo, Nov. 24, 2017, Bailey, Regina. (2017, November 24). Three Domain System. Retrieved from Bailey, Regina. "Three Domain System." ThoughtCo. (accessed December 16, 2017).