Abstract: Based on the antifungal activity screening of endophytic fungi obtained from Pyrethrum cinerariifolium,the strain of Y2 with higher activity was primarily identified and its active substances were separated. The primary morphological characteristics identification indicated that Y2 belonges to Fusarium sp..The extracts of Y2 fermentation liquid with high antifungal activity were eluted by acetone and ethyl acetate. The bioassay results showed that the inhibition rates of 10 time diluted fermentation liquid of Y2 against 6 pathogenic fungi including Exserohilum turcicum et al.were ranged from 80.41% to 93.26%,and that of the 5 time diluted fermentation liquid of Y2 against Botrytis cirerea and Glomerella cingulata were more than 80%. The antifungal activity of fermentation product of Y2 were analyzed by in vivo assay, the protective effect against B. cinerea and Lycopersicon esculentum were more than 50%,the therapeutic effect were not prominent .