Introduction: This study aimed to identify airborne fungi in São Luis, Maranhão, Brazil, to determine the prevalent genera and to correlate these genera with the area and season. Methods: In total, 1,510 colony-forming units (CFUs) of airborne fungi were isolated from the north, south, east and west sides and from the center of the city from January to December 2007. The samples were collected on Petri dishes that were exposed to the fungi by the gravitational method. Results: Twenty genera of fungi were isolated; the most common were Aspergillus (33.5%), Penicillium (18.8%), Cladosporium (14.2%), Curvularia (10.6%) and Fusarium (7.6%). The CFUs of the fungi were statistically significant (p < 0.0001). Fungal biological diversity was present all year, without any large seasonal variations but with slight increases in May, August and September. Conclusions: The fungal genera identified in this study were correlated with natural systems and could be useful when evaluating the impact of environmental changes on the region.