Morphological and molecular characterization of antagonistic ability of Trichoderma species was studied. Soil dilution plate method was used to isolate trichoderma from rhizosphere of bean, cowpea, cucumber, wheat and faba bean plants. Based on morphological and cultural characteristics, the Trichoderma isolates were identified as T. harzianum (10 isolates), T. koningii (8 isolates), and T. viride (2 isolates). A portion of rDNA, 560-600 bp was amplified from six biocontrol isolates using ITS1 and ITS 4 primers, and was sequenced and aligned against ex-type strain sequences from TrichoBlast and established Trichoderma taxonomy. Molecular phylogenetic analysis were performed based on nucleotide sequences in order to examine these isolates among 15 accession numbers of Trichoderma spp. found in GenBank. The results indicate that the FUE3, FUE5, FUE6, FUE9 and FUE18 Trichoderma isolates are closely related to Trichoderma koningii, while FUE15 isolate is closely related to Trichoderma harzianim .This result was in accordance with the result obtained from morphological and cultural characteristics. Production of volatile inhibitors and mycoparasitism were investigated using in vitro and in vivo tests in dual culture PDA medium and infected soils. The percent inhibitory effect against growth of Rhizoctonia solani was calculated, T. koningii FUE3 showed the greatest antagonistic effect to the pathogen (57.77%) in vitro experiment whereas T. koningii FUE6 and FUE18 were gave the highest reduction 96% of disease incidence caused by R. solani in greenhouse conditions.