Abstract: In this research we showed the effect of salinity (NaCl-free, 0.5 and 1%) on growth, photosynthesis, nitrogenase activity and antimicrobial effects in cyanobacterium Fischerella sp. FS18. In this way Fischerella sp. FS18 was treated with different concentrations of NaCl (0, 0.5 and 1%). Aqueous, petroleum ether and methanol extracts of the strain were examined against four bacteria and two fungi for antimicrobial purposes. The results indicated that the growth of Staphylococcus epidermidis PTCC 1114 was inhibited by all treatments. Aqueous extract did not have any inhibitory effect on Bacillus subtilis PTCC 1204. None of the treatments had decreasing effect on gram negative bacteria Entrococcus feacalis ATCC 8043 and Escherichia coli PTCC 1047. Among the fungi, Candida kefyr ATCC 1140 was more sensitive. Regarding physiological responses, the growth rate was higher in NaCl-free and salinity did not inhibit growth of other treatments. Similar results were seen in the case of other physiological processes. The light-saturated photosynthetic rate was higher in NaCl-free and it decreased with increasing salinity. With respect to nitrogenase activity, the highest rate belonged to NaCl-free and the cultures with higher growth rates reached to the maximum level of activity sooner. There was no significant difference between 0.5 and 1% NaCl treatments in relation to nitrogenase activity.