All stages are found in lungs and because they cannot be cultured ex vivo, direct observation of living Pneumocystis is difficult.

The trophozoite stage is thought to be equivalent to the so-called vegetative state of other species (such as Schizosaccharomyces pombe), which like Pneumocystis, belong to the Taphrinomycotina branch of the fungal kingdom.

Fluid leaks into alveoli, producing an exudate seen as honeycomb/cotton candy appearance on hematoxylin and eosin-stained slides.

At first, the name Pneumocystis carinii was applied to the organisms found in both rats and humans, as the parasite was not yet known to be host-specific.

The organism was named thus in honor of Czech parasitologist Otto Jirovec, who described Pneumocystis pneumonia in humans in 1952.

After DNA analysis showed significant differences in the human variant, the proposal was made again in 1999 and has come into common use.

[9] Pneumocystis species cannot be grown in culture, so the availability of the human disease-causing agent, P. jirovecii, is limited.

Hence, investigation of the whole genome of a Pneumocystis is largely based upon true P. carinii available from experimental rats, which can be maintained with infections.

The earliest report of this genus appears to have been that of Carlos Chagas in 1909,[12] who discovered it in experimental animals, but confused it with part of the lifecycle of Trypanosoma cruzi (causal agent of Chagas disease) and later called both organisms Schizotrypanum cruzi, a form of trypanosome infecting humans.

[17] The following year, Czech scientist Otto Jírovec reported "P. carinii" as the cause of interstitial pneumonia in neonates.

[18][19][20] Following the realization that Pneumocystis from humans could not infect experimental animals such as rats, and that the rat form of Pneumocystis differed physiologically and had different antigenic properties, Frenkel[21] was the first to recognize the human pathogen as a distinct species.

Recent studies show it to be an unusual, in some ways a primitive genus of Ascomycota, related to a group of yeasts.

In an intermediate classification system, the various taxa in different mammals have been called formae speciales or forms.