Pneumocystis carinii pneumonia is the most common opportunistic infection in AIDS, and accounts for significant morbidity and mortality in these and other immunocompromised patients. P. carinii is a eukaryotic microorganism of uncertain taxonomy that can infect numerous mammalian hosts. Developing from a small, unicellular 'trophozoite' into a 'cyst' containing eight 'sporozoites', its life cycle superficially resembles those seen both in the Protozoa and Fungi. Morphological and ultrastructural observations have lead some investigators to conclude that the organism is a protozoan, while others have felt that it more closely resembles a fungus. Phylogenetic relationships can be inferred from comparisons of macromolecular sequences. Small subunit ribosomal RNAs (16S-like rRNAs) are well-suited for this purpose because they have the same function in all organisms and contain sufficient information to estimate both close and distant evolutionary relationships. Phylogenetic frameworks based upon such comparisons reveal that the plant, animal and fungal lineages are distinct from the diverse spectrum of protozoan lineages. In this letter, phylogenetic analysis of Pneumocystis 16S-like rRNA demonstrates it to be a member of the Fungi.