This study was conducted to evaluate the antimicrobial activities of metabolites produced by endophytic fungi of ginseng plants. EtOAc extracts from endophytic fungi inhibited spore germination and pathogen growth. Among these, P. terrestris extract showed the best antimicrobial activity. Moreover, evaluation of molecular response by qPCR confirmed that genes involved in growth and virulence were down-regulated, leading to the growth inhibition. However, further studies need to be conducted to evaluate the in vivo potential of these extracts in ginseng pathogens.