Seven novel synthetic heterocyclic compounds containing naphthofurans were evaluated for their inhibitory effect on Phomopsis azadirachtae, the causative agent of destructive die-back disease of neem. Twigs of Azadirachta indica (Neem) infected with die-back were collected and were analyzed to determine the pathogen. Phomopsis azadirachtae the causal organism was isolated on malt extract agar from die-back infected neem twigs. 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 agent 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 causal organism of die-back of neem. Studies revealed a very effective in vitro control of P.azadirachtae mycelia growth at very significant concentration.