The Chilli strains (Capsicum annuum L.) were screened for pungency and non-pungency using a set of nine primers in five different combinations. Two primers combinations of CSF-1 and CSR-2, CSF-1 and CSR-4 were found to be robust primers capable of very low capsaicin detection. The study indicated that the SCAR primers provide simple, fast and economic means of early detection of pungency in capsicum.