Ninety species in addition to three species varieties belonging to thirty-one genera were isolated and identified from three economic plant roots (Saccharum officinarum, Corchorus olitorius and Triticum aestivum) on PDA and water agar at 28±2˚C. Fusarium (15 species, 45/60 samples and 31.4% of total fungi) and Aspergillus (15+2, 34/60 and 17%) were the dominant genera on PDA, whereas, Fusarium (13 species, 38/60 samples and 33.8% of total fungi) and Drechslera (6, 28 and 13.1%) were the commonest on water agar media. Of the previous genera F. udum, F. anthophilum, F. subglutinans, A. terreus var. aureus, A. flavus, D. biseptata and D. bicolor were the most detected species on PDA and WA. The endophytic fungi isolated belonging to anamorphic fungi (57 species, 23 genera of 11 order), Ascomycotina (26, 4 of 1) and Zygomycota (1, 1 of 1) on PDA and (38, 15 of 8) & (11, 2 of 1) belonging to anamorphic fungi and Ascomycotina on WA, while Zygomycota disappeared on WA.