We isolated a high efficient antifungal strain A02 from forest soil in a suburb of Beijing. The result of polyphasic taxonomy confirmed that strain A02 belongs to Streptomyces lydicus. The fermented broth of the strain presented a stable and strong inhibiting activity against many plant pathogenic fungi. The purpose of this study was to ascertain the substance base of the antifungal activity of strain A02. We extracted the antifungal metabolite of A02 by using column chromatography with X-5 macroporous resin and 200 mesh silica gel respectively, and then purified it by LC-9101 recycling preparative HPLC with a SP-120-15 column (JAIGEL-ODS-AP). An active compound with purity over 99.845% was finally obtained. The chemical structure of the active compound was determined with spectroscopy methods, including ultraviolet spectrometry, infrared spectrometry, high resolution mass spectrometry and nuclear magnetic resonance. According to the analysis results, we identified the active compound as a tetraene macrolide antibiotic with the molecular weight of 665, the molecular formula C33H47NO13 and the same chemical structure as natamycin. Our research revealed a new biosynthetic function for S. lydicus to produce natamycin, and an expanding application field for natamycin to be used for the control of fungal plant diseases.