Methanogens are anaerobic archaea that produce methane as a byproduct of their energy metabolism, i.e., catabolism. Methane production, or methanogenesis, is the only biochemical pathway for ATP generation in methanogens. All known methanogens belong exclusively to the domain Archaea, although some bacteria, plants, and animal cells are also known to produce methane. However, the biochemical pathway for methane production in these organisms differs from that in methanogens and does not contribute to ATP formation. Methanogens belong to various phyla within the domain Archaea. Previous studies placed all known methanogens into the superphylum Euryarchaeota. However, recent phylogenomic data have led to their reclassification into several different phyla. Methanogens are common in various anoxic environments, such as marine and freshwater sediments, wetlands, the digestive tracts of animals, wastewater treatment plants, rice paddy soil, and landfills. While some methanogens are extremophiles, such as Methanopyrus kandleri, which grows between 84 and 110 °C, or Methanonatronarchaeum thermophilum, which grows at a pH range of 8.2 to 10.2 and a Na⁺ concentration of 3 to 4.8 M, most of the isolates are mesophilic and grow around neutral pH.

Methanogens are usually cocci (spherical) or rods (cylindrical) in shape, but long filaments (Methanobrevibacter filiformis, Methanospirillum hungatei) and curved forms (Methanobrevibacter curvatus, Methanobrevibacter cuticularis) also occur. There are over 150 described species of methanogens, which do not form a monophyletic group in the phylum Euryarchaeota (see Taxonomy). They are exclusively anaerobic organisms that cannot function under aerobic conditions due to the extreme oxygen sensitivity of methanogenesis enzymes and FeS clusters involved in ATP production. However, the degree of oxygen sensitivity varies, as methanogenesis has often been detected in temporarily oxygenated environments such as rice paddy soil, and various molecular mechanisms potentially involved in oxygen and reactive oxygen species (ROS) detoxification have been proposed. For instance, a recently identified species Candidatus Methanothrix paradoxum common in wetlands and soil can function in anoxic microsites within aerobic environments but it is sensitive to the presence of oxygen even at trace level and cannot usually sustain oxygen stress for a prolonged time. However, Methanosarcina barkeri from a sister family Methanosarcinaceae is exceptional in possessing a superoxide dismutase (SOD) enzyme, and may survive longer than the others in the presence of O₂.

As is the case for other archaea, methanogens lack peptidoglycan, a polymer that is found in the cell walls of bacteria. Instead, some methanogens have a cell wall formed by pseudopeptidoglycan (also known as pseudomurein). However, most of methanogens have a paracrystalline protein array (S-layer) that fits together like a jigsaw puzzle. In some lineages there are less common types of cell envelope such as the proteinaceous sheath of Methanospirillum or the methanochondroitin of Methanosarcina aggregated cells.

In anaerobic environments, methanogens play a vital ecological role, removing excess hydrogen and fermentation products that have been produced by other forms of anaerobic respiration. Methanogens typically thrive in environments in which all electron acceptors other than CO₂ (such as oxygen, nitrate, ferric iron (Fe(III)), and sulfate) have been depleted. Such environments include wetlands and rice paddy soil, the digestive tracts of various animals (ruminants, arthropods, humans), wastewater treatment plants and landfills, deep-water oceanic sediments, and hydrothermal vents. Most of these environments are not categorized as extreme, and thus the methanogens inhabiting them are also not considered extremophiles. However, many well-studied methanogens are thermophiles such as Methanopyrus kandleri, Methanothermobacter marburgensis, Methanocaldococcus jannaschii. On the other hand, gut methanogens such as Methanobrevibacter smithii common in humans or Methanobrevibacter ruminantium omnipresent in ruminants are mesophiles.^{[citation needed]}

In deep basaltic rocks near the mid-ocean ridges, methanogens can obtain their hydrogen from the serpentinization reaction of olivine as observed in the hydrothermal field of Lost City. The thermal breakdown of water and water radiolysis are other possible sources of hydrogen. Methanogens are key agents of remineralization of organic carbon in continental margin sediments and other aquatic sediments with high rates of sedimentation and high sediment organic matter. Under the correct conditions of pressure and temperature, biogenic methane can accumulate in massive deposits of methane clathrates that account for a significant fraction of organic carbon in continental margin sediments and represent a key reservoir of a potent greenhouse gas.

Methanogens have been found in several extreme environments on Earth – buried under kilometres of ice in Greenland and living in hot, dry desert soil. They are known to be the most common archaea in deep subterranean habitats. Live microbes making methane were found in a glacial ice core sample retrieved from about three kilometres under Greenland by researchers from the University of California, Berkeley. They also found a constant metabolism able to repair macromolecular damage, at temperatures of 145 to –40 °C.

Another study has also discovered methanogens in a harsh environment on Earth. Researchers studied dozens of soil and vapour samples from five different desert environments in Utah, Idaho and California in the United States, and in Canada and Chile. Of these, five soil samples and three vapour samples from the vicinity of the Mars Desert Research Station in Utah were found to have signs of viable methanogens.

Some scientists have proposed that the presence of methane in the Martian atmosphere may be indicative of native methanogens on that planet. In June 2019, NASA's Curiosity rover detected methane, commonly generated by underground microbes such as methanogens, which signals possibility of life on Mars.