Ageratina adenophora is an invasive plant of global importance and has a broad distribution in the Western Himalayas. Endophtytic fungus Coniochaeta sp.F-8 was found in Ageratina adenophora. In this paper, we aim to investigate the antioxidative activity and cytotoxicity of the metabolites from Coniochaeta sp.F-8. Consequently, two compounds Phomoxanthone A and Penialidin A were isolated from the endophytic fungus of Ageratina adenophora for the first time. The structures of compounds were identified by IR, NMR and ESI-MS methods. Moreover, both of those compounds showed considerable antioxidative activity in vitro and resulted cytotoxicity in mouse embryo fibroblasts cell line Balb/c3T3. The present study provides a theoretical foundation for the development and utilization of endophytic fungi in Ageratina adenophora as a medicinal substance.