There were 66 isolates endophytic fungi were isolated from root,stem and leaf of Gingkgo.The results indicated that there was relationship between endophytic fungi quantity and tree age of Gingkgo,the older was Gingkgo,The more was endophytic fungi quantity.The metabolites of endophytic fungi were tested for anti-fungi activity,and the results showed that metabolites of 29 isolates could inhibit plant pathogenic fungi.The experiment indicated that endophytic fungi in Gingkgo have bioactivity for agriculture.