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<i>Fritillaria taipaiensis</i> P. Y. Li (<i>F. taipaiensis</i>) is a traditional Chinese herbal medicine that has been used for over two millennia to treat cough and expectoration. However, the increasing cultivation of <i>F. taipaiensis</i> has led to the spread of bulb rot diseases. In this study, pathogens were isolated from rotten <i>F. taipaiensis</i> bulbs. Through molecular identification, pathogenicity testing, morphological assessment, and microscopy, <i>Fusarium solani</i> was identified as the pathogen causing bulb rot in <i>F. taipaiensis</i>. The colonization of <i>F. solani</i> in the bulbs was investigated through microscopic observation. The rapid and accurate detection of this pathogen will contribute to better disease monitoring and control. Loop-mediated isothermal amplification (LAMP) and qPCR methods were established to quickly and specifically identify this pathogen. These results provide valuable insights for further research on the prediction, rapid detection, and effective prevention and control of bulb rot in <i>F. taipaiensis</i>.