Monitoring the microbiological quality of indoor air in hospital environments is a matter of comprehensive discussion due to its influence on the transmission and spread of pathogenic microorganisms. Among the artificially air-conditioned environments, hospitals are noteworthy for being specific places for the treatment and recovery of patients. In addition to problems related to patients health and professionals health, immunocompromised patients are more exposed to microorganisms present in the air currents of the refrigeration system in these environments, which can lead to consequences such as the occurrence of outbreaks. The objective of this work was to evaluate the indoor air quality in critical hospital environments of a teaching hospital in the city of Maceió, the state of Alagoas. In addition, we sought to identify the anemophilous fungal microbiota present. Air collections were taken in the rainy season, totaling, following recommendations indicated by Resolution No. 9 of the Brazilian National Health Surveillance Agency. The study was based on determining the concentration parameter of bioaerosols in indoor and outdoor air. The fungal microbiota identification was carried out by analyzing macro and microscopic characteristics for filamentous fungi and the use of molecular tools for yeasts. The most frequent species in hospital critical environments were Cladosporium cladosporioides, Penicillium piceum, Penicillium aurantiogriseum, Cladosporium herbarum and Aspergillus oryzae. In outdoor air, the most frequently found fungi were Penicillium sp., Aspergillus sp., and Cladosporium species. Candida tropicalis, C. krusei, and C. parapsilosis were identified among the yeasts in indoor and outdoor air samples. Identifying potentially pathogenic fungi in the evaluated environments points to the need for continuous monitoring of indoor air quality. Furthermore, to avoid the widespread fungal pathogens and the consequent occurrence of outbreaks, the adoption of indoor air microbiological quality analysis programs is suggested as an essential tool in developing infection control standards. In our study, airborne fungi are reported as indoor air contaminants in critical hospital environments. This finding is noteworthy because, in general, individuals present in these environments have an immunological impairment.