One of the pathogenic agents for live creatures are fungi. They have wide distribution and spores of them is everywhere, however, fungi as well as other organisms, are the pathogenic agents in shrimps. The best example for the diseases caused by fungi in adult and juvenile shrimps are Black gill disease and larval mycosis. In this study 578 specimen of Green tiger shrimp of Bushehr province area (Helleh site) were investigated. Totally 719 fungal colonies were isolated and identified from shrimp surface, gill, haemolymph, hepatopancreas and water of pools. The results of fungal identification were: 526 mould colonies, 179 yeast colonies, 12 strile mycelia and 2 unknown colonies. Aspergillus spp. (9.45%), Fusarium spp. (7.78%); Cladosporium spp. (6.35%), Aspergillus niger (6.11%), Rhodotorula rubra (5.98%), Aspergillus flavus (5.98%), Penicillium spp. (5.84%), Alternaria alternata (5.28%), Candida albicans (5.28%) and Candida spp. (5.14%) were dominant genera and species among the identified fungi in order of frequency, and 37.60% were other fungi species. None of the isolated Cladosporium spp. matched with pathogenic criteria. Two isolated (4.65%) of A. flavus are proved to be able to produce Aflatoxin.