The harsh environments of desert areas lead to natural selection of resistant creatures with obvious characteristics. This experiment looked for salt-tolerant fungi from native halophyte plants. Forty fungi isolated from three halophyte plant families that were collected from desert areas of Yazd Province in Iran, and the most tolerant isolates were selected at concentrations of 1, 2, 3, 3.5 and 4 molar sodium chloride. Five selected superior isolates were assigned to the phylum Ascomycota based on internal transcribed spacers sequences and β-tubulin gene, as well as morphological characteristics of the genus and species. Aspergillus terreusshowed superiority in terms of enzymes and antibacterial properties than other isolates. Other isolates were Acremonium, Paecilomyces, Microascusand Monosorascus. Aspergillus terreusalso showed antifungal efects against Aspergillus fumigatus, a human pathogen.