The procedure for staining arbuscular mycorrhizal (AM) fungal colonization in root tissues developed by Vierheilig et al. was modified by authors. Roots were cleared in 20% KOH for 40 to 120 min at 60℃ in water bath and then acidified by 5% acetic acid for 5 min. Cleared roots were stained for 30 min in 5% ink-vinegar solutions (Parker black writing ink, Quink) at 60℃ in water bath. Roots were destained by immersing in tap water for 14 h. Arbuscules of the AM fungi in root cortex were clearly visible and the distinctions between AM and other unidentified fungi could be noticed under a compound microscope. Moreover, lipid bodies within the hyaline hyphae of dark septate endophytes (DSE) were stained bright red and clearly distinguished when roots were restained in Sudan Ⅳ (60℃ for 60 min) and destained for 5 min in 70% ethanol. Stained roots could be mounted in glycerin jelly for making a permanent slide with high staining quality. This method should allow a large number of root samples of individual plant to be cleared and stained simultaneously and provided a simple, low toxic and inexpensive technique for staining AM fungi in cleared root for both wild and cultivated herbaceous plants with excellent staining results.