In this investigation, antimicrobial activity of Nostoc commune Vauch (isolated from agricultural wastewater canal, Beni Suef Governorate, Egypt) organic extracts were examined against nine selected microbial isolates. Four of them were Gram positive bacterial isolates (Bacillus subtilis, Mycobacterium phlei, Sarcina maxima and Staphylococcus aureus), four Gram negative bacteria (Escherichia coli, Proteus mirabilis, Pseudomonas aeruginosa and Salmonella arizonae) and one unicellular fungus (Candida albicans) were evaluated for their resistance against these extracts. Methanol was the best organic solvent for extraction of active material, rather than the other organic solvents. This material was produced, maximally, after 10 days of incubation in aerated shaken culture at 30ºC and pH 8.0 when N. commune was grown in Medium 18 growth medium. The antagonistic material was purified using thin layer chromatography then identified using chromatographic and spectroscopic techniques including UV, FT-IR, mass spectrophotometer and proton-NMR. Four unknown compounds were extracted that had long chain alcohol, sterol, long chain fatty acid and triterpen. These compounds were tested for their antimicrobial activity against B. subtilis. Only the long chain fatty acid (compound C) had an inhibitory effect on the growth of B. subtilis while the other compounds were not active.