The word "protozoa" (singular protozoon or protozoan) was coined in 1818 by zoologist Georg August Goldfuss, as the Greek equivalent of the German Urthiere, meaning "primitive, or original animals" (ur- ‘proto-’ + Thier ‘animal’). Goldfuss created Protozoa as a class containing what he believed to be the simplest animals. Originally, the group included not only single-celled microorganisms but also some "lower" multicellular animals, such as rotifers, corals, sponges, jellyfish, bryozoa and polychaete worms. The term Protozoa is formed from the Greek words πρῶτος (prôtos), meaning "first", and ζῶα (zôa), plural of ζῶον (zôon), meaning "animal". The use of Protozoa as a formal taxon has been discouraged by some researchers, mainly because the term implies kinship with animals (Metazoa) and promotes an arbitrary separation of "animal-like" from "plant-like" organisms.
In 1848, as a result of advancements in cell theory pioneered by Theodor Schwann and Matthias Schleiden, the anatomist and zoologist C. T. von Siebold proposed that the bodies of protozoans such as ciliates and amoebae consisted of single cells, similar to those from which the multicellular tissues of plants and animals were constructed. Von Siebold redefined Protozoa to include only such unicellular forms, to the exclusion of all metazoa (animals). At the same time, he raised the group to the level of a phylum containing two broad classes of microorganisms: Infusoria (mostly ciliates and flagellated algae), and Rhizopoda (amoeboid organisms). The definition of Protozoa as a phylum or sub-kingdom composed of "unicellular animals" was adopted by the zoologist Otto Bütschli—celebrated at his centenary as the "architect of protozoology"—and the term came into wide use.
's illustration of the Four Kingdoms of Nature, showing "Primigenal" as a greenish haze at the base of the Animals and Plants, 1860
As a phylum under Animalia, the Protozoa were firmly rooted in the old "two-kingdom" classification of life, according to which all living beings were classified as either animals or plants. As long as this scheme remained dominant, the protozoa were understood to be animals and studied in departments of Zoology, while photosynthetic microorganisms and microscopic fungi—the so-called Protophyta—were assigned to the Plants, and studied in departments of Botany.
Criticism of this system began in the latter half of the 19th century, with the realization that many organisms met the criteria for inclusion among both plants and animals. For example, the algae Euglena and Dinobryon have chloroplasts for photosynthesis, but can also feed on organic matter and are motile. In 1860, John Hogg argued against the use of "protozoa", on the grounds that "naturalists are divided in opinion—and probably some will ever continue so—whether many of these organisms, or living beings, are animals or plants." As an alternative, he proposed a new kingdom called Primigenum, consisting of both the protozoa and unicellular algae (protophyta), which he combined together under the name "Protoctista". In Hoggs's conception, the animal and plant kingdoms were likened to two great "pyramids" blending at their bases in the Kingdom Primigenum.
Six years later, Ernst Haeckel also proposed a third kingdom of life, which he named Protista. At first, Haeckel included a few multicellular organisms in this kingdom, but in later work he restricted the Protista to single-celled organisms, or simple colonies whose individual cells are not differentiated into different kinds of tissues.
Despite these proposals, Protozoa emerged as the preferred taxonomic placement for heterotrophic microorganisms such as amoebae and ciliates, and remained so for more than a century. In the course of the 20th century, however, the old "two kingdom" system began to weaken, with the growing awareness that fungi did not belong among the plants, and that most of the unicellular protozoa were no more closely related to the animals than they were to the plants. By mid-century, some biologists, such as Herbert Copeland, Robert H. Whittaker and Lynn Margulis, advocated the revival of Haeckel's Protista or Hogg's Protoctista as a kingdom-level eukaryotic group, alongside Plants, Animals and Fungi. A variety of multi-kingdom systems were proposed, and Kingdoms Protista and Protoctista became well established in biology texts and curricula.
While many taxonomists have abandoned Protozoa as a high-level group, Thomas Cavalier-Smith has retained it as a kingdom in the various classifications he has proposed. As of 2015, Cavalier-Smith's Protozoa excludes several major groups of organisms traditionally placed among the protozoa, including the ciliates, dinoflagellates and foraminifera (all members of the SAR supergroup). In its current form, his kingdom Protozoa is a paraphyletic group which includes a common ancestor and most of its descendants, but excludes two important clades that branch within it: the animals and fungi.
Since the protozoa, as traditionally defined, can no longer be regarded as "primitive animals" the terms "protists", "Protista" or "Protoctista" are sometimes preferred. In 2005, members of the Society of Protozoologists voted to change its name to the International Society of Protistologists.