Plants are usually exposed to different abiotic (climate changes, salinity… etc.) and biotic (pathogenic and/or toxicogenic micro-organisms, pests… etc.) stresses which limit the growth and productivity as well as cause considerable loss of worldwide agricultural production. We investigated the soil texture and moisture content and analyzed the chemistry of the cultivated soils in Upper Egypt. Examined soil has mean values of 1.4 % organic matter, 0.04 % total dissolved salts, and 7.17 pH. The moisture content of the samples was moderate (mean=15.75). All of the cultivated soil samples (100% of the samples) proved to be contaminated by filamentous fungi. A total of 148 fungal species + 7 varieties of 40 genera were isolated and identified using the dilution plate method. The gross fungal count was 653.7 colonies/mg of dry soil.  Aspergillus was the most dominant genus based on frequency (97.5% of the samples) and count (45.77% of the total fungal counts).  Penicillium had a second place (82.5% of the sample and 23.49% of gross count). Fusarium occupied the third place (67.5% and 6.55%).  Acremonium was one of the dominant genera (4^th place). It occurred in 45% of the samples examined and 5.95% of gross fungal counts. Curvularia and Humicola were moderate in frequency (30% and 25% of the samples) with low counts (1.53% and 4.04% of the fungal counts), and other genera were low and rare in frequency. Whereas sterile mycelium was high species in frequency (55% of the samples) but low in count (1.9% of fungal counts). Finally, the cultivated soils in this region, in general, are fertile but not completely healthy.