Monera has since been divided into Archaea and Bacteria, forming the more recent six-kingdom system and three-domain system. All new schemes abandon the Monera and now treat the Bacteria, Archaea, and Eukarya as separate domains or kingdoms.
Prior to the five-kingdom model with its Monera kingdom, these organisms were classified as two separate divisions of plants: the Schizomycetes (bacteria) were considered fungi, and the Cyanophyta were considered blue-green algae. The latter are now considered a group of bacteria, typically called the cyanobacteria and are now known not to be closely related to plants, fungi, or animals.
Although it was generally accepted that one could distinguish prokaryotes from eukaryotes on the basis of the presence of a nucleus, mitosis versus binary fission as a way of reproducing, size, and other traits, the monophyly of the kingdom Monera (or for that matter, whether classification should be according to phylogeny) was controversial for many decades. Although distinguishing between prokaryotes from eukaryotes as a fundamental distinction is often credited to a 1937 paper by Edouard Chatton (little noted until 1962), he did not emphasize this distinction more than other biologists of his era. Roger Stanier and C. B. van Niel believed that the bacteria (a term which at the time did not include blue-green algae) and the blue-green algae had a single origin, a conviction which culminated in Stanier writing in a letter in 1970, "I think it is now quite evident that the blue-green algae are not distinguishable from bacteria by any fundamental feature of their cellular organization". Other researchers, such as E. G. Pringsheim writing in 1949, suspected separate origins for bacteria and blue-green algae. In 1974, the influential Bergey's Manual published a new edition coining the term cyanobacteria to refer to what had been called blue-green algae, marking the acceptance of this group within the Monera.
In 1969, Robert Whittaker published a proposed five kingdom system for classification of living organisms. Whittaker's system placed most single celled organisms into either the prokaryotic Monera or the eukaryotic Protista. The other three kingdoms in his system were the eukaryotic Fungi, Animalia, and Plantae. Whittaker, however, did not believe that all his kingdoms were monophyletic.
In 1977, a PNAS paper by Carl Woese and George Fox demonstrated that the archaea (initially called archaebacteria) are not significantly closer in relationship to the bacteria than they are to eukaryotes. The paper received front-page coverage in The New York Times and great controversy initially, but the conclusions have since become accepted, leading to replacement of the kingdom Monera with the two kingdoms Bacteria and Archaea.