Allergy or asthma is triggered by inhaling allergens such as dust, mites, pet dander, pollens, and fungal molds. Samples were collected from various indoor environments including air conditioner filters, carpets, indoor plant soil, living room air, and pillow covers of residents living in air-conditioned flats for screening the fungal pollution of indoor environments and their role in allergies and asthma. This study included 30 residents with school-aged children suffering from allergies or asthma and a healthy control group of another 20 other residential indoor environments. The fungi isolated from indoor environments include Aspergillus niger, A. nidulans, A. flavus, A. fumigatus, Alternaria sp., Paeciliomyces species, Bipolaris species, Trichophyton verrucosum, and T. rubrum. Aspergillus species were isolated from all environments while Trichophyton species were only isolated from indoor plant soil. The fungal presence was higher in the indoor environments of group 1 with allergic rhinitis and asthma with a significant p-value <0.00001 showing its role in allergic rhinitis when compared the group 2 without allergy or asthma. The children suffering from allergies and asthma were further grouped into intermittent (70%), persistent (13%), and asthma or allergic asthma (17%) cases based on symptoms and duration. For the treatment of intermittent allergic rhinitis, a combination of oral antihistamines, and nasal decongestants were used, while persistent allergy symptoms were treated with corticosteroids (oral/intranasal), oral antihistamines, and oral leukotriene receptor antagonists. Asthma cases were treated with salbutamol sulfate, a bronchodilator, and oral leukotriene receptor antagonists with a combination of antiallergic treatments. A combination of treatments with improved indoor hygiene showed better relief for allergic rhinitis and asthma and was significantly reduced from persistent symptoms to intermittent or recovered from allergic symptoms.