The present work was carried out to study the effect of heavy metals from Collection station Mostorod Greater Cairo Egypt in Chlorella vulgaris and Scenedesmus quadricauda on amino acids content and ultrastructure. Results obtained revealed that the content of amino acids was increased gradually at all different concentrations of heavy metals (25%, 50%, 75% and 100%) compared to control. Cellular damage was studied by transmission electron microscope. It was observed that Chlorella vulgaris and Scenedesmus quadricauda when exposed to different concentrations of heavy metals revealed drastic changes in the overall ultrastructure such as the chloroplast separated far from the wall, the lamelly of the chloroplast appeared to be separated from each other, the pyrenoid disappeared and electro dense granular bodies identified as polyphosphate granules, appeared apparently in the cells. Damage to the algae ultrastructure was more severe with elevated heavy metal concentrations.These responses of Chlorella vulgaris and Scenedesmus quadricauda indicated their tolerance of heavy metal stress.