[Objective] We classified the antifungal strain Streptomyces sp. IMS002 that was isolated from the rhizosphere soil. We identified its bioactive compound in organic phase. [Methods] Through the concatenation analysis of 16S rDNA sequence and 5 concatenated sequences (atpD, gyrB, recA, rpoB and trpB), and physiological and biochemical detection, we classified Streptomyces IMS002. Besides, we observed the hyphae and spore morphology of sp. IMS002 by scanning electron microscope sp.. Using silica gel column chromatography, gel column chromatography and HPLC, we isolated and purified the active compound against Fusarium oxysporum. Furthermore, its chemical structure was determined by a liquid mass coupled high resolution mass spectrometer, a 500 MHz NMR spectrometer, and a circular dichroism spectrometer. [Results] Streptomyces sp. IMS002 had a close relationship with Streptomyces ambofaciens, and its fermentation broth had good antifungal activity against Fusarium oxysporum. With the separation and purification and modern spectrum identification, we identified this compound as Borrelidin. [Conclusion] Streptomyces sp. IMS002 produced Borrelidin that has bioactivity against Fusarium oxysporum.