Methanogens, also known as methanogenic archaea, are among the most ancient and widespread microorganisms, despite their particular requirements for growth. These oxygen-sensitive microorganisms have impacted climate and biogeochemical cycles throughout Earth’s history, although their specific roles in the long-term carbon cycle remain little explored. Methanogens evolved early during Earth’s history, likely during the Archaean Eon, in layered benthic microbial communities called microbial mats. These ancient mats, when lithified, form microbialites that represent some of the earliest evidence of life in the fossil record dating back > 3.5 Gy. Contemporary microbial mats experience a wide range of fluctuating conditions, including dramatic diel shifts in oxygen, sulfide, redox, temperature, salinity and pH. Methanogens are an integral part of marine and freshwater microbial mats and have been identified in the oxic zone of these sedimentary ecosystems; however, their adaptations to apparently unfavorable conditions and their role in long-term CO2 sequestration through precipitation of carbonate are unclear. Furthermore, the importance and coevolution of methanogens and microbial mats may explain the global role these organisms had on Earth’s major climate events during the Archean and Proterozoic eons, notably in the ending of icehouse periods and recovery of mats following mass extinctions – often in conditions with low or no oxygen. In addition to an important role in the evolution of our planet, methanogens may also produce biosignatures that are relevant for astrobiology research [and space exploration]. This review will discuss the diversity, physiology, and ecology of methanogens in order to clarify their role in biogeochemical processes through geologic time.