Antimicrobial activities of two cyanobacteria included; Synechococcus sp, Oscillatoria formosa and one filamentous green alga Spirogyra sp. were tested against 6 pathogens. All of three strains were isolated from Lake Kovada, Turkey. Cyanobacterial and algal cells were lyophilized and extracted with methanol, ethanol, ethyl acetate and water for the antimicrobial activity assays. Growth inhibition of bacteria] pathogens (Escherichia coli ATCC 11230, Pseudomonas aeruginosa ATCC 27853 Yersinia enterecolitica ATCC 1501, Staphylococcus aureus ATCC 29213, Bacillius subtilis ATCC 6633) and a fungal pathogen (Candida albicans NIHA 207) were tested with the algal extracts. No inhibition of bacterial and fungal growth occurred with aqueous extracts of the cyanobacteria or green alga. E. coli was not inhibited by organic extracts of 20 mg lyophilized cyanobacteria and alga, but these displayed a medium to strong inhibition of the growth compared to the other test bacteria. We observed good results from antimicrobial tests where extracts of 50, 100, 150 mg of lyophilized cells were used. Even the growth of E. coli was affected by the extracts of Spirogyra sp, Synechococcus sp. MALDI analyses of Oscillotoria formosa proved that no microcystin variants were present in lyophilized cells that might affect the growth of test bacteria.