Fungal infections of fish are widespread problem which affect wild and farmed species. The aim of the present study was to isolate and identify fungal flora in cultivated and natural Caspian Sea Acipenser persicus. The samples were obtained from skin, fin and gill of the fish and were inoculated into culture media with antibiotics and incubated at 23±1 ?C. 13 species of fungi isolated from the fishes including: Alternaria alternata, Cladosporium carioni, Mucor spp., Aureobasidium spp., Penicillium citrinum, Penicillium frequentans, Penicillium notatum, Paecilomyces spp., Aspergillus flavus, Aspergillus fumigatus, pseudallescheria boydii, Rhodotorula rubrum and Fusarium spp. The most frequent one was Cladosporium carioni in cultivated (16.95%) and natural fishes (10.17%). While the most fungi were isolated from fin (40.68%), the lowest were isolated from skin (28.82%) of fishes.