Infection of the commercially important silkworm, Bombyx mori by a tachnid parasitoid, Exorista bombycis induced activation of genes and cellular responses associated with apoptosis in integumental epithelial cells. Composite cellular profile showed initial autophagy, intermediate endoplasmic reticulum degranulation and deformed nucleus as well as later DNA fragmentation indicating apoptosis. Two cell death-associated proteins, autophagy 5-like (Atg5L) and apoptosis-inducing factor (AIF), in addition to caspase, are identified from the infected integumental epithelium through mass spectrometric analysis. Genes encoding these proteins showed age-dependent activation after the infection as revealed by quantitative expression analysis. Atg5 showed early upregulation in association with signs of autophagy whereas AIF showed late upregulation in association with DNA condensation and fragmentation. Expression of AIF showed negative correlation with that of Atg5 after the infection. On the other hand, in control, caspase expression showed positive correlation with AIF expression indicative of regulated expression in normal larval epithelium, which was absent after infection. Activation of Atg5, AIF and caspase genes in close association with different cell death events revealed the synchronized differential expression of apoptosis-associated genes in response to the macroparasitism. Enhanced expression of Atg5, AIF and caspase genes coupled with the appearance of cell death symptoms indicate parasitism-induced activation of genetic machinery to modulate cell death events in the epithelium, which was hither to unknown in invertebrate systems.