Abstract:[Objective] The endophytic fungus Colletotrichum gloeosporioides Cg01, isolated from Huperzia serrata, can produce huperzine A (HupA) with a low yield. As the strain was subcultured for generations, the yield decreased and the strain degraded. Studies have shown that epigenetic modification is associated with the synthesis of secondary metabolites. This study aims to increase the yield of HupA, improve the quality of degraded strains, and decipher the mechanism of secondary metabolite synthesis from the perspective of epigenetic modification.[Methods] The carbon sources and biotic elicitors for the rejuvenation media were screened according to the colony morphology, mycelial growth rate, biomass, and HupA yield. The histone methyltransferase inhibitors UNC0224 and BRD4770 were screened to improve the HupA yield. The expression of genes involved in epigenetic modification was determined. [Results] The addition of the water extract of H. serrata did not significantly affect the growth rate, morphological characteristics, or biomass of C. gloeosporioides Cg01, while it increased the yield of HupA, which was 1.67 times (125.7 μg/L) that of the control group in the fifth generation. Furthermore, the addition significantly down-regulated the expression of the histone methyltransferase gene Cg12377, the histone deacetylase gene Cg15620, and the DNA methyltransferase gene Cg02440, while it up-regulated the expression of the histone deacetylase gene Cg02312. UNC0224 had no significant effect on the HupA production, while 2-15 μmol/L BRD4770 increased the HupA yield (152.10-169.57 μg/L) and down-regulated the expression of Cg12377, Cg02440, Cg02312, and Cg15620. [Conclusion] The secondary metabolite production of C. gloeosporioides Cg01 could be maintained by adding the water extract of H. serrata. The addition of BRD4770, a histone methyltransferase inhibitor, could increase the yield of HupA. This study provides a reference for addressing the strain degradation during the large-scale production of endophytic fungi and studying the influence of histone methylation on the synthesis of secondary metabolites.