The soil is the main habitat of saprophytic and pathogenic fungi. Heat, rainfall (humidity), soil ingredients are important factors in the growth of fungi. Soil-borne fungi are a major cause for different degrees of allergy or another fungal disease in human and animals. This study was carried out with the aim of isolation and identification of non-pathogenic and pathogenic fungi from the soil of Greater Tunb, Abu-Musa and Sirri islands, Persian Gulf, Iran. In this study, a total of 60 soil samples were collected from the three islands of Greater Tunb, Abu-Musa, and sirri. The soil suspensions were prepared by sterile physiologic saline (0.9% NaCl) and then antibiotics of penicillin and streptomycin were added and 0.2 ml of the suspension was added to Sabouraud’s dextrose agar medium containing chloramphenicol with and without cycloheximide and incubated at 27°C for 2-3 weeks. The fungal isolates were examined macroscopically and microscopically. A total of 483 fungal isolates including 30 genera were isolated as follows: Aspergillus spp. (22.99%), Mycelia sterilia (16.15%), Penicillium spp. (8.9%), Chrysosporium spp. (6.83%), Cladosporium spp. (5.6%), Fusarium spp. (4.97%), Alternaria spp. (4.76%), Acremonium spp. (3.73%) and other fungi (26.07%). In the current study, a fungus of Sporothrix schenckeii isolated from the soil of Greater Tunb and AbuMusa. The results of this study contribute towards a better understanding of the incidence pattern of soil-borne fungi, Given that no study has investigated this issue, the findings of the present study can be beneficial for the management of public health surveillance, epidemiologists as well as physicians.