In order to extract high quality protein sample for two dimensional electrophoresis (2-DE) assay,aqueous solution method,trichloroacetic acid-aceton method and the advanced phenol isolated method were used to extract the proteins from Rhizophora apiculata Bl,and the harvest rate,the integrality and the solubility of the three methods were compared and analyzed. The results showed that the colloidal deposition,which was composed of polysaccharide but little of protein,was isolated by the aqueous solution method; the proteins,which were isolated by trichloroacetic acid-aceton method,was purer than that from others and the background in 2-DE was most clearest,but the integrality of protein sample was not enough for 2-DE; 800—1000 μg protein deposition could be harvested from 500 mg leaves material by the advanced phenol isolated method,and the protein spots which were detected on 2-DE gel map were seven times than that by trichloroacetic acid-aceton method. These data demonstrated that the advanced phenol extraction method was more excellent than others based on the great protein harvest ratio and integrality.