Green alga cultures of Scenedesmus quadricauda were treated with different concentrations of clodinafop-propargyl herbicide (0, 10.5 21, 42 and 84 ppm). Transmission electron microscopy and total protein analysis were applied to clarify the resistance of herbicide. Photos of longitudinal section in algal cell wall showed clear response to different concentrations of the herbicide. The response appeared as change in cell shape and increase in cell size, as well as thickness in the layers forming the cell wall which may indicate a type of resistance mechanism. Total protein analysis showed inducing or inhibition of the synthesis of some polypeptide fractions by herbicide treatments. These polypeptide fractions may have a role in resistance mechanism. These results encourage using green algal cell suspension of S. quadricauda for screening of herbicide resistance.