Trichoderma species are useful, avirulent plant symbionts that act as bicontrol agents against phytopathogens. The identification of Trichoderma genes whose expression is altered during early stages of interaction with seedling roots is an important first step towards understanding the rhizosphere competency of Trichoderma. Differential display reverse transcriptase PCR have been developed by using RNA extracted from harvested mycelium during different colonization stages of tomato germinated seeds and roots. DDRT-PCR products were profiled on gel agarose and 62 differential bands excised, purified, cloned and sequenced. These EST sequences were related to known proteins by blastx and gene ontology search and submitted to dbEST database after confirmation. Most of transcripts corresponded to hypothetical proteins in different organisms specially fungi. A number of them corresponds to regulatory and functional proteins such as; putative beta-1,6-glucanase, secretion-related small GTPase, 40S ribosomal protein S3a, 3-hydroxybutyryl-CoA Dehydrogenase, DNA repair protein rad50, lipid phosphate phosphatase-related protein type 3, nucleolar essential protein, 3\\\\\\\\\\\\\\\'-5\\\\\\\\\\\\\\\' exonuclease/helicase, slingshot homolog 2b, TOM7 family protein, phospholipase A2, fatty acid desaturase, nuclear pore complex subunit Nup133, ubiquitin-activating enzyme, 3\\\\\\\\\\\\\\\'-5\\\\\\\\\\\\\\\' exonuclease/helicase, set-15 protein and 60S ribosomal protein L40. Some of these transcripts corresponded to those whose expression is already altered under relatively similar interactions in Trichoderma and mycorrhiza fungi.

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