Five isolates of Trichoderma spp., three  belonging to T. harzianum and two belonging to T.viride were isolated from cotton seedlings  infected with damping –off or from rotted roots of adult plants. The isolates were evaluated for biocontrol capacity against 14 isolates of  Fusarium solani  involved in seedling damping –off, of  cotton under greenhouse conditions. Analysis of variance showed very highly significant effects of Trichoderma spp. isolates. F. solani  isolates, and their interaction on pre-emergence damping- off,  post-emergence damping-off, survival, plant height, and dry weight. Responses of F. solani  isolates to antagonistic effects of Trichoderma isolates  were different.Some  isolates of F. solani  exhibited response to all Trichoderma isolates, which siginifficantly increased the percentage of surviving seedlings, plant height and dry weight. Cluster analysis of Trichoderma spp. isolates based on antagonistic patterns showed that isolates were placed in two groups. The first group included isolates of T. harzianum, while the second group included isolates of T. viride. The results of cluster analysis of F. solani  isolates,based on their response patterns to Trichoderma spp. Isolates. Placed the isolates in three distinct groups;however, grouping the isolates was not related to geographic origins. It is worth noting that isolates of Middle Egypt and Upper Egypt were  placed in same group.