Aluminum (Al) toxicity often exists in plants growing on acid soils, limiting crop production therein. Microscopic techniques are commonly used in the research on Al toxicity in plants. A comparison study was carried out of the advantages and disadvantages of three microscopic techniques, hematoxylin staining method, fluorescent staining method and electronic microscopic scanning method, using growing under Al stress. Results show that the hematoxylin staining method could distinguish difference in morphologic variation of root tips between two different cultivars of lespedezas and between different Al treatments. The fluorescent staining method could detect differences between plants in control and in Al treatments, and make it convenient to observe mucilage on root surface and Al distribution in apoplast. The electronic microscopic scanning method could make out differences between the plants in control and in Al treatments, but could not find out difference in Al tolerance between cultivars of lespedezas through energy spectrum analysis.