Endophytic fungi play important roles for host's stress tolerance including invasion by pathogenic microbes. Small molecules are common weapons in the microbe–microbe interactions. Panax notoginseng is a widely used traditional Chinese medicinal plant and harbors many endophytes, some exert functions against pathogens. Here, we report six new compounds named myrothins A–F (1–6) produced by Myrothecium sp. BS‐31, an endophyte isolated from P. notoginseng, and their antifungal activities against pathogenic fungi causing host root‐rot disease. Their structures were elucidated with analysis of spectroscopic data including 1D and 2D NMR, HR‐ESI‐MS. Myrothins B (2) and E (5) showed the weak activity against Fusarium oxysporum and Phoma herbarum, and myrothins F (6) showed weak activity against F. oxysporum.