This study was conducted to determine fungal spores in the indoor air of the houses in the city of Afyon, Western-Anatolia, Turkey. We investigated the seasonal properties of mould spores in 10 houses of Afyon over a period of one year. Viable moulds were recovered from all 10 houses. Twenty seven different moulds were isolated and identified from the indoor air of the houses. The most common genus was Cladosporium, spp. (31.9%), followed by Aspergillus spp. (18.6%), Penicillium spp.. (15.5%), Alternaria spp. (13.0%) and other species (21.0%). The mould concentration was higher in the kitchens than in other parts of the houses such as the living rooms and bedrooms (p < 0.05). The fungal flora of the air in the Afyon city region has a seasonal variation. All fungal species had their highest prevalence in summer and their lowest in winter, but only Aspergillus spp. had a significant seasonal variation (p = 0.012). Viable moulds are common in the houses of Afyon. Reducing these indoor fungi is necessary to improve the health of individuals with fungal-induced diseases like asthma.