Abstract: The objective of this study was to explore whether the fungus of swainsonine-secret exist in locoweeds and rhizosphere soil, identify genus of those fungus and determinate their swainsonine yield in Qinghai Province and Inner Mongolia Autonomous Region. Fungus was isolated from the locoweed and soil samples, and swainsonine was detected by thin layer chromatography and gas chromatography for isolated fungus. Two strains of endophytic fungi produced the alkaloid swainsonine were isolated and obtained from locoweeds and rhizosphere soil, and named FS-5 and EFG-7, and SW yield is 0.773 and 0.11 mg·g^-1, respectively. Morphological evidence and sequence analysis of the ITS region suggest that FS5 is most closely related to Schizophyllum sp, and EFG-7 is Fusarium tricinctum. The results showed that the fungus of swainsonine-producing exist in locoweeds and rhizosphere soil in Qinghai Province.