Extremophiles are organisms that can thrive under extreme environmental conditions. In this study, isolated and identified fungal genera and their species from Red Sea saline soils in Upper Egypt were carried out. Soil texture, moistures content, organic matter, total dissolved salts and pH value of the soil in addition to some mono- and bi- equivalent elements were analyzed for the samples. 1% glucose-Czapek’s agar medium was used for isolation of filamentous fungi. A total of 42 fungal species + 3 varieties of 11 genera were collected and identified that have the ability to survive under extremophilic conditions. Majority of isolated species belonged to genus Aspergillus (15 sp. + 2 var. and 32.12% of gross fungal counts) and Penicillium (13 sp. and 54.05%), whereas Acremonium (1sp. and 4.60%) and Emericella (2 sp. +1 var. and 3.35%) were less. Nine species of 7 genera were listed in rare frequency of occurrence (≥ 10 % of the samples), with very low in counts (collectively, 5.03%). The organic matter content of saline soils had positive effect in flourishing of filamentous fungi with depression in pH value of the soils.