The identification of Trichoderma genes whose expression is altered during early stages of interaction with developing roots of germinated seeds is an important step towards understanding the rhizosphere competency of Trichoderma spp. The potential of 13 Trichoderma strains to colonize tomato root and promote plant growth has been evaluated. All used strains successfully propagated in spermosphere and continued their growth in rhizoplane simultaneously root enlargement while the strains T6 and T7 were the most abundant in the apical segment of roots. Root colonization in most strains associated with promoting the roots and shoots growth while they significantly increased up to 43% and 40% roots and shoots dry weights, respectively. DDRT-PCR has been developed to detect differentially expressed genes in the previously selected strain; Trichoderma harzianum T7, during colonization stages of tomato germinating seeds and roots. Amplified DDRT-PCR products were analyzed on gel agarose and 62 differential bands excised, purified, cloned and sequenced. Obtained ESTs were submit-queried to NCBI database by blastx search and gene ontology hierarchy. Most of transcripts (29 EST) corresponds to known and hypothetical proteins such as; secretionrelated small GTPase, 40S ribosomal protein S3a, 3-hydroxybutyryl-CoA Dehydrogenase, DNA repair protein rad50, lipid phosphate phosphatase-related protein type 3, nuclear essential protein, phospholipase A2, fatty acid desaturase, nuclear pore complex subunit Nup133, ubiquitin-activating enzyme and 60S ribosomal protein L40. Also, 13 of these sequences showed no homology (E-value>0.05) with public databases and considered as novel genes. Some of these ESTs corresponded to genes encodes enzymes potentially involved in nutritional support of microorganisms which have obvious importance in the establishment of Trichoderma in spermosphere and rhizosphere, via potentially functioning in acquisition of nutrients from energy-rich carbon compounds leaked from the germinating seeds and roots

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