Some isolated taxa showed preference for specific tissues types. Previous studies in other plants have also indicated that endophytes exhibit tissues specificity. As expected, tissue specificity of fungal endophytes was demonstrated in our study. Particular endophytes were only found in one tissue, which suggests that certain species survive within the specific chemistry or texture of different tissues . The diversity and species richness of endophytic fungi were higher in the underground part (roots) than that in the above-ground parts (stems, leaves, and seeds). Some similar results have been reported in the previous studies. The possible reasons are that soil-borne fungi are typically more prevalent and diversified than those that infect aerial plant tissues , and there are abundant nutriments in roots of P. notoginseng that are suitable for the growth of fungi. The relative abundance of each fungus identified in P. notoginseng reflects an unequal distribution of isolate richness among species. Similar results have been found in other plants, such as Stellera chamaejasme and Taxus globose