There is a recent trend towards the use of eco-friendly biological control agents for protecting crops from pest and disease, especially soil-borne plant pathogens, as an alternative to existing chemical methods. Among various biocontrol agents, Trichoderma, which has multiple mechanisms for the biocontrol of phytopathogens, is used widely. The present study explores the role of Trichoderma sp. in inducing cytological changes in fungal plant pathogens during parasitization. In dual culture plates, all the fungal isolates (SE₆, KT₆, KT₂₈, and BRT₁₁) along with a standard culture of T. harzianum were able to antagonize and mycoparasitize two soil-borne fungal phytopathogens (Sclerotium rolfsii and Rhizoctonia solani) of chickpea wilt complex. The suppression of S. rolfsii was slower than that of R. solani. The interaction between T. harzianum and sclerotia of S. rolfsii was studied by light microscopy and transmission electron microscopy (TEM). Ultra-structural examinations revealed that growth and development of Trichoderma resulted in extensive host cell alterations, such as retraction, aggregation and disintegration of cytoplasmic contents. Lysis and deformation of hyphal cell wall, degradation and disappearance of cytoplasmic contents and loss of cellular integrity in sclerotia of S. rolfsii paratisized by T. harzianum is clearly apparent from transmission electron micrographs.