FOR THIS STUDY, samples were collected from seedlings infected with damping-off or root rot in adult cotton plants from different locations in the Giza governorate. The samples yielded 25 fungal isolates. The isolates were identified as Rhizoctonia solani (44%), Fusarium spp. (44%) and Macrophomena phasolina (12%). In the pre-emergence stage of the cotton seedlings, 24 fungal isolates were pathogenic on cultivar Giza 90, while all fungal isolates were pathogenic on Giza94 compared to the control. On Giza90, F. fujikuroi F10 (80%), R. solani RS9 (100%), M. phasolina M4, and M12 (34%) were the most pathogenic isolates. On Giza 94, F. fujikuroi F10 (100%), R. solani RS9 (100%), M. phasolina M4 (64%) were the most pathogenic isolates. In the post-emergence stage of Giza 90, Fusarium isolate F1 (22%), R. solani RS11 (18%), M. phasolina M4, and M12 (48%) were the most pathogenic isolates. On Giza 94, Fusarium isolate F1 (16%), R. solani RS4 (14%), and M. phasolinaM4 (24%) were the most pathogenic isolates. All fungal isolates were pathogenic and decreased the survival percentage of the two cultivars. On Giza 90, F. fujikuroi F10 (0%), R. solani RS9(AG2-2) (0%), and M. phasolina M4 (18%) were the most effective isolates in decreasing survival. On Giza 94, F. fujikuroi F10 (0%), R. solani RS9(AG2-2) (0%) group, and M. phasolina M4 (16%) were the most effective isolates in decreasing survival. The most effective fungal isolates that decreased plant height and dry weight for both cultivars were F. fujikuroi F10, RS9(AG2-2), and M4.