ORGANIC pollution is prominent environmental issue concerning ……. water pollution in the world. It is important to reveal the effects of organic pollutants on algal growth and toxin production for assessing ecological risk of organic pollution. Polyacrylamide gel electrophoresis (SDS-PAGE) was tested as an analytical tool for the isolation and identification of the protein. The treatment of Pterocladia capillacea and Ulva lactuca with chloramphenicol, clofibric acid, acetyl salicylic acid, nonylphenol and bisphenol stimulated the synthesis of (three and eight) high molecular masses polypeptides, respectively, (five and six) low molecular masses polypeptides, respectively. On the other hand, inhibition of 31.51and 12.30 KDa protein inPterocladia capillacea and Ulva lactuca after the same treatments, respectively. Examination of electron micrographs of Pterocladia capillacea and Ulva lactuca pharmaceutical treated cells reflected damages in chloroplast structures, which manifested by a change in the thylakoid number, rupture, and dissolving of thylakoid membranes. In addition, the disintegration of the chloroplast in some parts, the appearance of necrotic areas, deformation in the cell wall as well as deformation in the morphology of the cells are clear.