Endophytes are referred to fungi colonizing in healthy plant tissues without causing overt symptoins in or apparent injury to the host. Research results in recent years show that endophytes can produce some metabolites same or similar to those from the host plant, and metabolites with the novel structure and specific bioactivity.Macleaya cordata is Chinese traditional herbal drug with plenty of alkaloid, which has pharmacologic function of antibacterial action and so on.In this paper, we selected macleaya cordata as our materials to isolate and identify its endophytes.By plant microecology and plant pathology methods, we have studied the composition and distribution of Macleaya cordata endophytic fungi, and discussed its biological function and disease resistance, aiming to offer initial value of development and utilization of the Macleaya cordata endophytes. The result showed that endophytic fungi of macleaya cordata had abundant diversity, which belonging to 5 families、11 genera, Including the dominant strain:Penicillium Aspergillus, separation rates were 1.06%,0.91%, Followed by colletotrichum separation was 0.83%. Different organs of macleaya cordata have diversity in quantity and population. The leaves had the greatest population of endophytic fungi. The distribution of the endophytic fungi varied in different height and in different season.Taking chestnut dry rot fungi, tea-leaf wheei spot fungi, ligustrum vicaryi melasma fungi and laurel blossom vane spot as indicate fungi, the bacteriostasis effect of macleaya cordata endophytic fungi were analysed using pair-culture method. J91 strains which had stronger inhibit activity on four pathogenic fungus were separated. Biological characteristic and antifungal activity of J91were studied, the result showed J91 had obvious control effect of ligustrum vicaryi melasma fungi. The antifungal composition exist in extrazellular and intrazellular. The ribosomal DNA internal transcribed spacer (ITS rDNA) region was amplified and sequenced to identify J91, it was distinguished as BotryospHaeria.