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Sesamum indicum L. is highly vulnerable to biotic stresses in which charcoal rot disease cuased by Macrophomina phaseolina is one of the major constraints of sesame yield. In response to pathogen infection plant produces a large amount of secondary metabolites like PR proteins, phenolics and other signaling compounds. In present investigation the role PR proteins β-1,3 glucanases and chitinases during host-pathogen interaction was studied at different time interval i.e. 0, 24, 48 and 72 hours post inoculation. Maximum induction of β, 1-3 glucanases was found at 48hpi in resistant genotypes than the susceptible. However maximum chitinase induction was noted in susceptible genotypes at 48 hpi. The expression of both genes was studied by quantitative real time PCR which was also supported the biochemical enzyme assay.