The use of air cleaners has become popular to quickly remove contaminants present in indoor air such as fine dust and fungi. However, fungal information is rarely available in the filters equipped in the air cleaners. This study was conducted in winter to examine fungal concentration and species in the air cleaner filters of ten residential houses located in Incheon, Seoul, Hwaseong, and Gimpo cities. Fungi were detected in nine out of eleven filters from the ten houses. The level of fungi in the filters ranged from 0 CFU/cm2 to 2,370 CFU/cm2. There were differences in the fungal concentration among the eleven filters. Filters from three houses revealed levels over 1,000 CFU/cm2. The operation time of air cleaners did not seem directly related to the level of fungal concentration. A total of 326 isolates were obtained and classified as six genera belonging to Alternaria, Aspergillus, Cladosporium, Fusarium, Penicillium, and Trichoderma. Among these six genera, 20 species including one Alternaria, one Aspergillus, three Cladosporium spp., two Fusarium spp., eleven Penicillium spp., and two Trichoderma were identified. There were species that cause allergic reaction, pneumoniae, mycosis, and plant disease. Three species were known species of mycotoxin producers. Aspergillus niger, Cladosporium cladosporioides, and Penicillium brevicompactum were the most frequently detected fungi both in the air and in the air cleaner filters. This is the first report of fungal communities present in the air cleaner filters of residential houses in Korea.