This study explored whether seasonal and/or climatic factors influenced detection of specific genotypes of Pneumocystis jirovecii. Between 1989 and 2001, 155 isolates of P.jirovecii were obtained from patients undergoing bronchoscopic alveolar lavage. For each isolate, the month and climatic conditions were noted. Genotypes of P.jirovecii were distinguished by polymorphisms in the mitochondrial large-subunit rRNA gene. There were monthly and seasonal variations in the frequency of detection of mixed genotypes (p0.018 and p0.031, respectively) and genotype 2 (p0.029 and p0.086, respectively). There was no association between month/season and genotypes 1, 3 and 4, or between monthly temperature or rainfall and any genotype. © 2007 European Society of Clinical Microbiology and Infectious Diseases.