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Growth, morphological changes, amino acid composition, total soluble protein, and protein electrophoretic pattern were monitored for Scenedesmus obliquus and Nitzschia perminuta grown in the presence of different concentrations of Co2+ and Ni2+. Lower concentrations of cobalt stimulated the dry mass production and total soluble protein content of the two algae, whereas higher concentrations were inhibitory. Generally, N. perminuta showed more tolerance to the phytotoxicity of the two metals than S. obliquus and more tolerance to nickel than cobalt. However, S. obliquus seems to be more tolerant to cobalt than nickel. Cobalt and nickel have induced an increase in cell volume, change and disorder in cell shape. The increase in cell volume was much observed in Ni2+ treated cells. At the same time, the two metals did not induce any distinct morphological abnormalities in N. perminuta. Co2+ has stimulated the biosynthesis of all free amino acids in S. obliquus, except aspartic acid and phenylalanine, whereas Ni2+ caused 22% inhibition in the content of total free amino acids, except cystine and arginine. On the other hand, Co2+ has reduced the content of free amino acids in N. perminuta, except cystine, methionine, valine, and lysine. On the other hand, Ni2+ stimulated the biosynthesis of glycine, alanine and histidine and highly stimulated valine and sulphur containing amino acids (cystine and methionine) in N. perminuta. High cobalt concentration (4 ppm) resulted in the disappearance of 28.7 kDa protein, 3.5 ppm Ni2+ stimulated the appearance of 18 and 20 kDa proteins in S. Obliquus, while 37 kDa proteins disappeared from N. perminuta treated with high doses of Co2+ and Ni2+. [Copyright &y& Elsevier]