Abstract: Cyanobacterial cultures isolated from diverse environment of acidic condition were studied for their tolerance mechanism. The identified predominant genera of Anabaena, Westiellopsis and Nostoc were taken for study. Among the acid tolerant cyanobacterial cultures, a protein of 15.7 kDa was identified in the cyanobacterium Nostoc sp. governing for acid tolerance mechanism. The N terminal sequencing of the desired protein were done to construct a suitable primer for the identification of desired gene. This may serve as a tool in engineering them onto suitable saline tolerant effective nitrogen fixers making them a good candidature for all type of soils thus directly influencing the productivity of rice.