Silver nanoparticles possess unique  physical, chemical, and biological properties which find myriad applications but the random application of silver nanoparticles may arise many problems particularly on benefits biotechnological agent T. harzianum which serves as bio-control and growth promoting agents for many crop plants. The results indicated that AgNPs possess antifungal properties against T. harzianum and the antifungal activity increased with increasing their concentrations. Electrophoretic analysis was performed to determine the effect of AgNPs on T. harzianum protein profile. Protein migration in this study demonstrated that nanoparticles caused changes in the protein profiles. Two bands completely disappeared after treatment with 100 and 200 ppm of AgNPs with molecular weights 140, 27 and 21.0 kDa. The genotoxicity exhibited by AgNPs was demonstrated by DNA fragmentation post treatment particularly at high concentrations of the nanoparticles. The fragmented bands increased with increasing AgNPs concentrations. 2, 5 and 7 fragmented bands with different molecular bands were detected at 50,100 and 200 ppm of AgNPs respectively. Three bands with molecular weight 1000,900 and 750 bp were detected at 100 and 200 ppm of AgNPs. Also, the result showed that AgNPs treated fungal cells both accumulated more intracellular glucose and trehalose than the compound-untreated cells. Also, the result showed that T. harzianum treated with AgNPs increased extracellular glucose and trehalose than the compound-untreated cells as a result of cell wall damage.