Pneumocystis fungi are closely related unicellular, low-virulence microorganisms occurring commonly in the lungs of humans and many other mammalian species. The transient primary colonization by these opportunistic fungi mainly affects the upper respiratory tract and most often occurs in adolescence. Recolonization, manifested by Pneumocystis pneumonia (PCP), may occur in the immunocompromised individuals or may result from other accompanying infectious disease. The major risk factor for PCP development is the reduced count of CD4+ T cells. Investigations of the biology of Pneumocystis fungi have long been limited due to the lack of a reliable and reproducible method for their in vitro cultivation. Nevertheless, the clinical characteristics have been described based on observations of both human and animal cases. These fungal infections can be symptomatic as well as subclinical or latent, which is common in rats, mice, guinea pigs, rabbits, cats, sheep, and various species of wild animals. An important role as a reservoir of these fungi is played by dogs. Such breeds as smooth and wire-haired Miniature Dachshunds, Miniature Spitz dogs, and English Toy Spaniels are especially predisposed to colonization by these fungi. This article presents the characteristics of fungi from the genus Pneumocystis, with particular emphasis on the life cycle of these pathogens. The other aspects discussed, are the current diagnostic and therapeutic challenges associated with this infectious disease.