Archaea were first classified as a separate group of prokaryotes in 1977 by Carl Woese and George E. Fox in phylogenetic trees based on the sequences of ribosomal RNA (rRNA) genes.
Leta 1965 sta Linus Pauling in Emile Zuckerland predlagala nov način razvrščanja glede na zaporedja (sekvence) nukleotidov, ki kažejo sorodstvene odnose med organizmi.