This study was done to indicate the exertion of secondary metabolites of cyanophyta algal excerpt for Fischerella muscicola which isolate from one of the running water systems in Tikrit City nearby Tikrit University campus. Study the effectiveness of secondary metabolites in Fischerella muscicola ethanol extract to inhibition species of different bacterial and fungi,The Fiscerella muscicola protein extract showed inhibitory activity, as a basic dose of 10,000 micrograms/ml was given at 21 mm for Escherichia coli, and 7,000 micrograms/ml gave a maximum dose of 16 mm for and a concentration of 5000 µg/ml E.coli, diameter 15 mm.