Seven novel synthetic heterocyclic compounds contai ning naphthofurans were evaluated for their inhibitory effect on Phomopsis azadirachtae, the ca usative agent of destructive die-back disease of neem. Twigs of Azadirachta indica (Neem) infecte d with die-back were collected and were analyzed to determine the pathogen. Phomopsis azadi rachtae the causal organism was isolated on malt extract agar from die-back infected neem tw igs. They were identified by PCR based molecular methods. Phomopsis genus specific primers (5.8S r-DNA) were then used for the confirmation of P. azadirachtae – the causative age nt of die-back of neem by Polymerase chain reaction (PCR). Studies revealed the amplification of expected 141bp DNA in P. azadirachtae isolated from the diseased trees confirming the cau sal organism of die-back of neem. Studies revealed a very effective in vitro control of P.aza dirachtae mycelia growth at very significant concentration.