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Background: The fungal part of the pulmonary microbiome (mycobiome) is understudied. We report the composition of the oral and pulmonary mycobiome in participants with COPD compared to controls in a large-scale single-centre bronchoscopy study (MicroCOPD)., Methods: Oral wash and bronchoalveolar lavage (BAL) was collected from 93 participants with COPD and 100 controls. Fungal DNA was extracted before sequencing of the internal transcribed spacer 1 (ITS1) region of the fungal ribosomal RNA gene cluster. Taxonomic barplots were generated, and we compared taxonomic composition, Shannon index, and beta diversity between study groups, and by use of inhaled steroids., Results: The oral and pulmonary mycobiomes from controls and participants with COPD were dominated by Candida, and there were more Candida in oral samples compared to BAL for both study groups. Malassezia and Sarocladium were also frequently found in pulmonary samples. No consistent differences were found between study groups in terms of differential abundance/distribution. Alpha and beta diversity did not differ between study groups in pulmonary samples, but beta diversity varied with sample type. The mycobiomes did not seem to be affected by use of inhaled steroids., Conclusion: Oral and pulmonary samples differed in taxonomic composition and diversity, possibly indicating the existence of a pulmonary mycobiome., Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: Einar M. H. Martinsen, Elise O. Leiten, Ingvild Haaland, Gunnar R. Husebø, Kristel S. Knudsen, and Christine Drengenes declare no conflict of interest. Walter Sanseverino and Andreu Paytuví-Gallart are employed at Sequentia Biotech SL. Rune Nielsen reports grants from the Endowment of Timber Merchant A. Delphin and Wife (The Norwegian Medical Association) and grants from GlaxoSmithKline during the conduct of the study, and grants and personal fees from AstraZeneca, grants and personal fees from GlaxoSmithKline, grants and personal fees from Boehringer Ingelheim, and grants from Novartis outside the submitted work. Tomas M. L. Eagan reports grants from Helse Vest (Western Norway Regional Health Authority) during the conduct of the study, and personal fees from Boehringer Ingelheim outside the submitted work. This does not alter our adherence to PLOS ONE policies on sharing data and materials.