Anabaena variabilis was collected by isolation from saline soil at Elhamol city, Kafr Elsheikh governerate, Egypt. Spirulina platensis was obtained from cyanobacteria Lab., Microbiology Dept., Sakha Agricultural Research Station, Egypt. GC/MS analysis showed that 37 and 7 bioactive compounds from A. variabilis and S. platensis were identified, respectively. Moreover, the area percentage of the same bioactive compound varied according to the type of cyanobacteria. The major phytochemical constituents in the methanol extract of A. variabilis are Pentadecanoic acid 29%, 12,15-Octadecadienoic acid methyl ester 10.26%, Hexadecenoic acid methyl ester (Z) 8.3%, Thieno [3,4-C] pyridine,1,3,4,7-tetraphenyl 5.86%. While, S. platensis methanol extract contain Hexadecanoic acid 29%, 9,12,15-Octadecadienoic acid methyl ester 24% and 9,12 Octadecatrienoic acid zz methyl ester, 24.36%.