When two strains of bacteria (Pseudomonas aeruginosa and Stenotrophomonas maltophilia) were tested on seedlings of cotton cultivar Giza 86, they did not show any significant effects on plant height and dry weight. The two bacterial strains were also nonpathogenic (0.0 % infection). The Pseudomonas aeruginosa strain was more effective in reducing damping-off symptoms caused by Fusarium oxysporum isolates no_s 1 and 2 whereas, S. maltophilia was effective against F. oxysporum isolate no. 4. Although the two bacterial strains reduced damping-off on cotton seedlings caused by Fusarium fungal isolate no. 3, P. aeruginosa was more effective than S. maltophilia. Fusarium oxysporum isolates no_s. 1 and 2 significantly reduced plant height than isolates no_s. 3 and 4. Strain of S. maltophilia significantly increased dry weight of cotton seedlings when soil was infested with isolates no_s 3 or 4 of F. oxysporum. In vitro antagonism tests showed that P. aeruginosa inhibited growth of F. oxysporum isolates. The inhibition ranged from 19.33 to 31.0 %. On the other hand, S. maltophilia did not show any inhibition of F. oxysporum isolates growth. The two bacterial strains did not show any significant effects on the activities of peroxidase and polyphenol oxidase, while the ß- 1, 3 glucanase activity was significantly increased. The total and reduced sugar contents were significantly increased due to the application of the two bacterial strains but P. aeruginosa was more effective. Pseudomonas aeruginosa was the only strain which significantly increased free phenols.