Eleven isolatesbelonging to genus Trichoderma were isolated from the rhizosphere of watermelon roots grown at different localities in Egyptian soil. They were morphologically identified as T. harzianum, T. hamatum, T. glaucum, T. reesei and T. viride. These five species comprised different eleven isolates which were originated from different localities. significant differences in radial growth of the different pathogens tested. Also, there was a significant difference between the pathogens in dual culture and the control treatment which include the pathogen only. Results lead us to conclude that DNA based RAPD provide a reliable method for grouping isolates of Trichoderma spp < em>. In addition, analyzing phyllogenetic similarities among isolates based on DNA pattern according to RAPD technique. Genomic DNA prepared from the eleven Trichoderma spp < em>. isolates was used to screen primer for readily detectable and reproducible polymophic PCR amplifications. The PCR conditions employed, allowed amplification of many bands on the agarose gel. Bands present in each sample were scored for presence and absence of amplification products. UPGMA cluster analysis divided in two subclusters; the first one included the T. harazianum isolates. However, the second cluster included the T. hamatum and T. glaucum isolates. Meantime, eachisolate of T. reesei and T. viride fall in one another subcluster showing the lowest similarity with other isolates. Results conclude that the differences in DNA profiles among isolates of Trichoderma species not related to their geographic origin or biocontrol ability. The biocontrol ability of the tested isolates of Trichoderma species under greenhouse condition, against the different pathogens using the susceptible watermelon cultivar Giza 1 were studied. Results obtained showed the effectiveness of all isolates of Trichoderma species in this respect. Results also showed the superiority of T. harzianum and T. hamatum isolates as well as T. reesei in some cases against the tested pathogens.