Background: Fungal spores are ubiquitous constituents indoors and outdoors and are now generally identified as important causes of respiratory allergies. Objectives: This study aims to evaluate the frequency and prevalence of allergens with fungal origin at homes of allergic patients with respiratory symptoms in the city of Mashhad, Iran. Methods: In this cross-sectional study, a group of patients with allergic rhinitis (n = 50) were selected based on positive skin prick test. Healthy volunteers with no respiratory allergy were included in control group with the same age as diseased group. Samples from nasal cavity and different parts of bedroom were collected and cultured. The fungal agents were recognized by conventional mycological methods based on the cultural and microscopic appearance as properties. Results: Colonization with fungi was obtained in 26% -64% and 86-98% of the patient and healthy groups, respectively. Among all species isolated from specimens of the patients, A.flavus was dominant which followed by A. niger, Penicillium and Cladosporium whereas the most commonly isolated fungi from the whole specimens of healthy subjects were A. flavus, A. fumigatus, A. niger, Penicillium, Yeast, Alternaria and Cladosporium. Conclusions: Fungi can be hazardous for health. Furthermore, prevention of fungal spores' growth is important, and also identifying and determining the most common allergen fungi are key steps to provide the necessary recommendations to the patients in controlling and preventing disease.