Pneumocystis carinii f. sp. hominis is an important cause morbidity and morality, causing P. carinii pneumonia (PCP) in AIDS and other immunocompromised patients. Long thought of as protozoan, molecular analysis of the ribosomal gene locus first demonstrated that P. carinii is a member of the fungal kingdom. Currently P. carinii is considered to be fungus likely to Ascomycetes, based on its ultrastructure, certain elements of its cellular biology, and nucleotide sequences of main genetic loci. The standard method for diagnosis P. carinii is microscopic examination of stained (immunofluorescent or conventional tinctorial) invasive specimens: BAL (bronchoalveolar lavage), lung biopsy or induced sputum with sensitivity varying range from <50% to >90%. Molecular detection system have the potential to provide a higher degree of sensitivity than microscopic method. PCR technique have been applied to lower respiratory tract clinical specimens and recently to non-invasive oral washes as well. Because P. carinii infection can be rapidly progressive and success of therapy dependent to the time of the initial therapy, early diagnosis and treatment is essential.