Stem rot disease caused by fungal pathogen, Sclerotium rolfsii Sacc., is potential threat to groundnut production in warm and humid condition. After host-pathogen interaction, a multitude of plant resistance associated reactions are initiated. In the present investigation we studied the role of polyamines and ethylene during host-pathogen interaction in stem rot tolerant (CS319, GG17 and GG31) and susceptible (TG37A) groundnut genotypes at 24, 48 and 72 h after infection. Stem rot tolerant genotypes showed higher expression of polyamine biosynthesis genes ornithine decarboxylase (Ordec), spermine synthase (Sms) and lipoxygenase1 (LOX1) gene at 72 h after infection than that of susceptible genotype TG37A. The expression analysis of ethylene biosynthesis genes (1-aminocyclopropane-1-carboxylate oxidase: ACCO and (ACCS) showed up regulation in stem rot susceptible genotype TG37A than that of tolerant genotypes after infection at all stages (24, 48 and 72 h after infection). The expression of amine oxidase (AMO) gene was observed highest in stem rot susceptible genotype TG37A while minimum in GJG31. Expression of this gene was remarkably induced in TG37A which may leads to higher accumulation of H2O2. Higher content of a polyamine, putrescine was found in the leaves of stem rot tolerant genotypes at 48 and 72 h after infection. These results implied that tolerant genotypes induced higher polyamine biosynthesis which may involve in plant defense and impart tolerance/ resistance. While, susceptible genotype (TG37A), utilized higher flux of S-Adenosyl methionine (SAM) for ethylene biosynthesis which may leads to necrosis of plants. Thus, stem rot resistant genotypes may be developed through genetic manipulation of polyamine biosynthesis pathway