The fungal flora contains diverse organisms including a large number of fungi, molds, mushrooms, yeasts, rusts, and smuts etc. Airborne fungi are important source of indoor allergens and studies confirm their role in the development of allergic diseases. In order to identify indoor fungal allergens, 539 house dust samples were collected from different regions in Saudi Arabia. Samples were analyzed by culture employing Sabouraud Dextrose and Potato Dextrose Agar. The cultivated plates were incubated at 25°C up to 5 days. Colony forming units (CFU) were enumerated and identified.Various fungal species were identified from the samples. The majority of fungi identified belonged to the allergenic genera. Aspergill us niger constituted 38.5%, A. fumigat us 15.5%, Rhizopus spp 14.5%, Penicillium spp 8%, Aspergill us spp 7.1%, Alternaria spp 4.4%, Yeast 4%, Mucor 3%, Cladosporium spp 2%, Fusarium spp. 1%, and other minor type include A. flavus 2%. The noncoastal cities (n=455) showed a higher percentages than coastal cities (n=84) because of difference in sample collection.Public places, primarily mosque, was included in the study. Out of 104 samples, Aspergill us niger constituted 39%, Rhizopusspp 14%, Aspergill us fumigat us 12%, Alternaria spp 10%, Fusarium sp. 8%, Penicillium spp 6%, As pergill us spp 6%, Ulocladium, Bipolaris and Yeast 2%, Mucor, Cladosporium spp and Drecslera spp. 1%.Exposure to certain fungal species cause sensitization and allergic reactions and may increase severity of asthma symptoms. Therefore, proper avoidance strategy need to be adopted with a regular cleaning of storage area and humidity control measures, if possible.