Background: Bulb rot causes loss of the perennial medicinal plant Fritillaria przewalskii Maxim., is exacerbated with growth years and seriously constrains plant productivity, but the pathogens responsible for the disease were still unknown, very few reports were presented before.Methods: To determine potential pathogenic sources, fungus strains were isolated from diseased plant samples with bulb rot symptom of the 3- to 5-year-old F. przewalskii plants by tissue separation, and assayed for pathogenicity according to Koch’s Law.Results: Seven pathogenic strains (F1-F7) were detected in5-year-old rot bulbs, six (F1-F6) in 4-year-old rot bulbs, and four (F1, F2, F5, F6) in 3-year-old rot bulbs. All of the strains were able to infect bulbs by stabbing and some exhibited varying levels of aggressiveness. Relative to the non-stabbing controls, the bulbs stab-inoculated with F5, F2, F7, F4, F1, F6, and F3 showed 76.65%, 75.15%, 71.44%, 40.37%, 39.09%, 36.87%, and 34.93% rot after 8 days, respectively. Phylogenetic analysis revealed that theses trains (deposited in GenBank under accessions MH917682 to MH917688) were clustered into Bionectria ochroleuca (F1, F3, F4), Fusarium oxysporum (F2, F7), Fusarium tricinctum (F5), and Clonostachys rosea (F6). The two species of Fusarium had the strongest pathogenicity, followed by Bionectria ochroleuca and Clonostachys rosea. Although leading to low bulb rot incidence by stab-inoculation, F1 showed the highest isolation rate (48.9%) among all strains. Conclusions: Thus, the edible and medicinal bulbs of F. przewalskii are susceptible to synergetic contamination by these seven pathogenic strains at some point after their third year of growth, which has contributed to the species endangered status, with the two strains of Fusarium being the predominant pathogens. To our knowledge, this is the first report on the seven strains of four fungal species causing in F. przewalskii bulb rot in China.