Karnal bunt (KB) disease incited by Tillelia indica is widely distributed and an economically important disease of wheat. The present study, attempts were made to find out the physiological, biochemical and molecular basis of resistant and stage specific immunity, against KB.The enzymes of phenylpropanoid pathway were expressed and remained higher in resistant genotype. Phenylpropanoid metabolism is involved in synthesis of carotenoid, act as precursor of ABA synthesis. The low carotenoid levels in resistant than susceptible genotype due to its more conversion in to ABA pool, induced downstream jasmonic acid mediated pathway and caused induction of PR- proteins (b-1,3 glucanase, protease and protease inhibitors) in wheat spikes. Stoichiometric balance of protease and protease inhibitor play key role in controlling the resistance by intervention of programmed cell death (PCD). The results of present study clearly demonstrated that resistant is due to involvement of multi component signaling leading to genotype to genotype dependent and stages dependent immunity against KB and cystatin-proteinase interaction is key factors in triggering plant defence against pathogenic fungi.