In search for ecofriendly alternatives to chemical pesticides, the study was conducted to find the toxicity of a partially purified extract of an endophytic fungus Schizophyllum commune using Spodoptera litura (Fabricius) as a model. Toxicity was assessed by cytotoxic analysis using fluorescence microscopy on third instar larvae of S.litura fed with the same concentrations. In addition, various morphological deformities in larvae, pupae and adults were also recorded, after feeding second instar larvae to a diet supplemented with partial purified fungal extract up to a prepupal stage. The results showed various morphological deformities in larvae, pupae and adults. In cytotoxic effect, a significantly lower number of living haemocytes and a very high number of apoptotic and necrotic cells were observed in larvae treated with partial purified fungal extract for different time intervals (24hr, 48hr, 72hr and 96hr). The extent of recovery of cytotoxicity caused by the fungal extract was almost negligible indicating its long term effect. Overall the study highlights the significance of pesticides which are biologically originated, eco-friendly and safe.