Toxicity of copper (Cu+2) and cadmium (Cd+2), as pollutants, in sea water was evaluated using two microalgae, Chlorella salina and Nannochloropsis salina. Experiments were carried out for 96 h with the two heavy metals causing changes in the growth, protein pattern and DNA profile of the studied algae. Lethal concentration (LC50) values for Cu+2 and Cd+2 indicated that both C. salina and N. salina are affected by Cu+2 than Cd+2. Polyacrylamide gel electrophoresis (SDS PAGE) was used for the separation and identification of proteins. The treatment of the two marine microalgae with Cu+2 and Cd+2 prompted the disappearance of a single band of C. salina and four bands of N. salina protein profiles, compared to control. From the phylogenetic tree that resulted, moderate genetic similarity was detected for untreated and heavy metals treated C. salina samples (52%), while low genetic similarity was detected for untreated and heavy metals treated N. salina samples (10%). Random amplified polymorphic DNA (RAPD) technique was used for investigating variability in genetic pattern of DNA in both C. salina and N. salina. In this regard, from the genetic pattern of DNA, it was concluded that both copper and cadmium induced some genotoxic influences in both algal species, with more genotoxic effect of copper than cadmium.