38 strains of endophyte fungi belong to 9 genera were isolated from the stem of medicinal plant Eucommia ulmoides Oliv.collected in Qinling Mountain by the methods of tissue separation.Penicillium was the dominant group and Paecilomyces,Alternaria,mycelia sterilia were the common groups.The result of antimicrobial activity assay showed 61% endophyte fungi presented antibacterial activity,34% endophyte fungi presented antifungals activity towards Algernaria alternata,Colletotrichum gloeosporioides and C.capsici.It indicated antimicrobial activity was common in endophyte fungi isolated from E.ulmoides Oliv.and worthing for further studying in biological control of plant diseases.