Prokaryotes were treated as one fundamental group, with organisms now called archaea classified among the bacteria.

By the mid-twentieth century, biologists often divided cells into two broad types. Eukaryotic cells, such as those of animals and plants, contain a nucleus. Prokaryotic cells do not. Organisms in that second group were generally treated as bacteria.

That meant methane-producing microbes and other organisms now called archaea were classified as unusual kinds of bacteria. Under a microscope, the grouping was understandable: both bacteria and archaea are small cells without nuclei.

Carl Woese and George Fox looked deeper. In 1977, they compared ribosomal RNA. Because parts of it change slowly over evolutionary time, its sequence can reveal very ancient relationships.

The methane-producing microbes were not simply an odd bacterial branch. Their ribosomal RNA differed so strongly that it pointed to a separate major lineage. Later molecular work reinforced the distinction, and Archaea came to be recognized alongside Bacteria and Eukarya as one of the three domains of cellular life.

The word prokaryote is still useful for describing cells without nuclei. What changed is the idea that all such cells form one natural evolutionary group or are all bacteria.