Acute exacerbations of chronic obstructive pulmonary disease (COPD) results in increased mortality and can be triggered by a range of factors, including microorganisms. Very little studies have examined the role of fungi and fungal diversity in COPD patients. The aim of the study was to determine the role of Candida in COPD during an exacerbation. Oral swabs, sputum, feces and whole blood samples were collected from the AECOPD patients and control group. Mycological and serological analysis were performed. Yeast were statistically significantly more often isolated from the AECOPD group (97.06%) than from the control group (26.32%). 7 species were isolated from the AECOPD, and 3 from the control group. Dominated Candida albicans followed by C. tropicalis. α-diversity was much greater in AECOPD patients than in controls. β-diversity was also assessed. A much higher level of antimycotic resistance was observed in isolates from the AECOPD group, which affects the effectiveness of therapy. Serological tests showed twice the frequency of positive results in the AECOPD group. The mycobiota of AECOPD patients is numerically and taxonomically richer than controls, including species less frequently recorded in humans. Our research confirms that fungal mycobiota may be a potential factor influencing the development of exacerbations and progression of COPD.