In search for ecofriendly substitute to chemical pesticides, the present study was conducted to find the toxicity of a partially purified extract of an endophytic fungus Schizophyllum commune on Spodoptera litura (Fabricius). Toxicity was assessed by cytotoxic analysis using fluorescence microscopy on third instar larvae of S. litura. In addition, various morphological deformities in different life stages of S. litura (larvae, pupae and adults) were also recorded, after feeding second instar larvae to a diet having partial purified S. commune extract up to a prepupal stage. The results showed various morphological deformities in different life stages (larvae, pupae and adults) of the insect. In cytotoxic analysis, living cells percentage was highly reduced however apoptotic and necrotic cells percentage significantly increased in larvae fed with partial purified fungal extract for different time intervals (24hr, 48hr, 72hr and 96hr). The recovery of cytotoxicity induced 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.