Cyanobacteria are rich sources of bioactive compounds. In the present study, the antifungal activity of different solvent extracts of Microcystis aeruginosa was evaluated. Among these extracts, diethyl ether extract showed the highest antifungal activity against all tested mycotoxigenic fungi and gave inhibition zone ranged from 10.3 to 21.6 mm. In this direction, the fraction (F4) was the best fraction in antifungal activity against all tested fungi. Sub-fraction F4-10 was chosen as the highest sub-fraction had bioactivity. Using TLC bioautography, GC-MS and NMR; two antifungal compounds were isolated, purified and identified as Butylated Hydroxytoluene (BHT) and Hexadecanoic acid, methyl ester.