There are many fungi could be isolated from cotton seeds. In this research the following fungi were isolated: Alternaria alternate, Aspergillus flavus, Aspergillus niger, Aspergillus ochraceous, Cephalosporium sp., Fusarium moniliforme, Fusarium oxysporum, Fusarium semitectum, Fusarium solani, Penicillium sp., Rhizoctonia solani, Rhizopus sp., Stemphylium sp., Trichothecium sp. and Verticillium sp. Pathogenicity test showed that Fusarium oxysporum, Fusarium solani, Fusarium moniliforme and Rhizoctonia solani were the most devastative fungi on cotton seeds. The use of trisodium orthophosphate (1.9 g L1) significantly, reduced the incidence of the ungerminated seeds, post-emergence damping off and the abnormal seedlings. Soaked seeds prior to the sawing followed by 3 times of spraying cotton seedlings with the target antioxidant or formulated antioxidants GAWDA® formulation at the rate of 2.2 g L1 significant increased the contents of chlorophyll a, b, carotenoid and total phenols in the plant leaves at the age of (30, 45, 60, 75) days old. Plant height, shoot and root lengths, shoot and root weights, number of cotton bolls, number of branches% and weight of bolls were increased by 30.05, 29.90, 80.34, 82.20, 86.53, 121.08, 168.80, 242.96 and 140.54%, respectively. Plant dry weight was increased by 82.24%, cotton seed yield by 142.77% and lint cotton was increased by 22.09%. The quality of the cotton fibers including; Micronair, length (mm) UHM, Regularity %, Durability gm/tex, Elongation%, the degree of color reflection (Rd) and the degree of yellowing b+ were also increased by 19.49, 4.00, 6.36, 16.95, 9.35, 11.86 and 6.49%, respectively. These results are persuasive evidence directed to cotton growers to apply this method for controlling seed-borne fungi of cotton, improve cotton yield, promote the quality of the cotton fibers, as well as increase the seed cotton production and subsequently the extracted oil.