The response of cowpea seeds grown under salinity-induced stress conditions to different cyanobacterial extracts of two strains (Aphanizomenon flos-aquae and Phormidium sp.) was studied during seed germination. The results indicated that aqueous extract was more stimulating to germination than organic extract where higher levels of germination percentage, enzymatic activity, nucleic acid, protein and total soluble sugars contents were obtained. In addition, the indicators of stress such as proline content, lipid-peroxidation and relative permeability of the root membranes were lower than the organic extract. Application of aqueous cyanobacterial extracts of Aphanizomenon flos-aquae and Phormidium sp. stimulated seed germination and the metabolic activities of salt-stressed and unstressed seeds, while the lipid-peroxidation and relative permeability of the root membranes were reduced. Therefore, aqueous algal extracts alleviated the harmful effect of salinity stress on seed germination. This can be used on a vast scale as an inexpensive and eco-friendly farming policy to counteract the hazardous effect of salinity on plants especially during the critical period of seed germination where salinity can inhibit it either partially or completely.