Fungi are ubiquitous eukaryotic organisms and are transient flora in air. Their persistence and viability in air over time make them potentially pathogenic especially in environments like daycare facility (crèches). The fungal load in fifty selected crèches in Ado-Ekiti and the effectiveness of commonly used disinfectants on the fungi isolated were investigated. Fungi isolates were recovered from the air in crèches facilities environments using sedimentation method and were identified using morphological and cultural methods. Their susceptibility to different disinfectants: Izal, Dettol, Z-Germicide and Nixoderm was evaluated using broth dilution method. A total of one hundred and sixty-four isolates belonging to 10 fungal genera: Alternaria, Candida, Cladosporium, Fusarium, Mucor, Nigrospora, Penicillium, Pullularia, Rhizopus and Trichoderma were recovered from crèches. Alternaria sp. was the most predominant. It was also observed that the isolates exhibited varying levels of sensitivity to the different disinfectants. Z-germicide was the most effective though with fungicidal activities at, and above the manufacturer’s recommended in-use concentrations. However, the fungal isolates were observed to show resistant to all tested concentrations of Izal. The results of the present study clearly showed that airborne fungi of public health significance were present in crèches and as such may pose threats to health of the babies. Proper hygiene should be practiced in crèche environments to prevent fungal diseases among the babies.