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The microbiota refers to all the microorganisms living in and on the human body; its fungal component is known as the mycobiota. The molecular component (mycobiome) has been linked to certain pulmonary diseases. Morphological fungal examination is still common practice and makes it possible to isolate fungi on direct examination or after sample culture. This study aimed to identify fungi via the genus colonising the respiratory tract in our environment and to evaluate the relationship between identified fungi and underlying diseases. We performed a retrospective study of patients who underwent bronchofiberoscopy and mycological analysis of fluid collected by broncho-alveolar lavage at our centre over a period of 5 years. During the study period, 1588 samples from 1547 patients were analysed (50.7% male, mean age 63.7 ± 14.8 years). Among the 1588 samples, 213 (13.4%) were positive on direct examination, and 1282 (80.8%) were positive after culture. The average number of species detected per sample was 1.4 ± 1.1. For patients with positive fungus, the median was two (ranging from one to seven). At least three fungal species were isolated in 14.4% of samples (17.9% of positive cultures), and at least two were isolated in 41.2% of samples (51.1% of positive cultures). Sterile mycelium was observed in 671 samples (42.28%), while Candida was identified in 607 samples (38.25%), and Geotrichum was identified in 271 samples (17.08%). Moulds were more frequently associated with bronchiectasis, while yeasts were associated with infectious pneumonia. Both moulds and yeasts were less frequent in diffuse interstitial lung disease, and yeast was less frequently present in chronic cough. Although overall, sterile mycelium and Candida were most frequently observed regardless of the underlying disease, there was nonetheless significant variability in the fungal genera between diseases. Fungal spores are highly prevalent in respiratory samples in Martinique. The species present in the samples varied according to the underlying respiratory disease. [ABSTRACT FROM AUTHOR]