Archaea were discovered during research that aimed to understand the fundamental evolutionary relationships of all extant life. Bacteria have been studied since the 17th century and, until relatively recently, taxonomy was based on characterizing morphological and physiological properties of organisms grown in laboratory culture. The advent of molecular biology led to new approaches for defining taxonomic and evolutionary relationships. In the late 1970s, Carl Woese and George Fox discovered, through the comparison of gene sequences encoding ribosomal RNA (rRNA), that all “bacteria” were placed within two distinct groups, rather than one: the Eubacteria (including most prokaryotic species grown in the laboratory) and the Archaebacteria, later termed “Archaea” to reflect their distinct evolutionary history from (Eu)Bacteria. At the time, an important feature of cultivated archaea was that they were generally found in environments that were considered to represent extremes of temperature, salinity, pH or oxygen availability at which life could be sustained. Although this view was maintained for around fifteen years following the discovery of Archaea, the application of molecular techniques in microbial ecology in the 1990s revolutionized scientists’ understanding of archaeal diversity. Molecular signatures of archaea (16S rRNA genes) were found in all “non-extreme” environments, including soils, sediments, marine, and freshwater habitats. During the past twenty years, scientists have come to recognize that Archaea represent a major proportion of microbial biomass on the planet and make unique and essential contributions to biogeochemical cycles.