Introduction and objective. Nosocomial invasive fungal infections, particularly aspergillosis, are an increasing problem in immunocompromised patients. The presented study evaluates fungal diversity and the presence of Aspergillus in air samples from two hospitals. Materials and methods. Over the course of one year (rainy and dry seasons), the air was sampled from three areas in two hospitals (1 and 2) using a single-stage Andersen viable particle sampler (Thermo Scientific, Waltham, MA, USA). The fungi were identified by macro-and micromorphology, and the number of colony forming units (CFU)/m 3 air and their richness, abundance, and diversity were determined. Isolates Aspergillus genus were characterized by their thermotolerance. Results. The CFU/m 3 air was similar at both hospitals during the two seasons, but different between the sampled areas. Results showed 10 fungal genera for hospital 1, and 8 for hospital 2. The most abundant were Penicillium, Cladosporium and Aspergillus. The thermotolerance test confirmed the identification of A. fumigatus section Fumigati. The highest growth rate was found in Aspergillus section Nigri. Conclusion. Determining the fungal diversity in the two hospitals was important because all the species have the potential to be pathogenic, especially the section Fumigati.