Abstract:[Background] Root rot is highly susceptible to the cultivated Aconitum carmichaelii Debx. in Jiangyou area of Sichuan, China. The plants wither and die after being infected by root rot, which ultimately affects the yield of medicinal materials. The prevention and treatment of the root rot are difficult due to complex pathogenic factors and the diversity of pathogenic fungi. [Objective] To identify the pathogens of root rot on A. carmichaelii Debx. cultivated in Jiangyou area, and to provide theoretical basis for diagnosis and prevention of the disease. [Methods] Pathogen isolation was carried out by means of diseased tissue isolation method. Koch’s rule was used to prove the pathogenicity of fungal strain isolated from A. carmichaelii. The pathogens were identified based on their morphological characteristics and rDNA-ITS sequence. [Results] Forty-seven fungi isolates were isolated from the root rot of A. carmichaelii. Strains GF3-3, GF3-6 and GF6-1 were the causal pathogen fungi of the root rot of A. carmichaelii. The pathogen strains GF3-3, GF3-6 and GF6-1 were identified as Fusarium solani, F. oxysporum and F. proliferatum via morphological characteristics and rDNA-ITS sequence. [Conclusion] Fusarium solani, F. oxysporum and F. proliferatum were the principal pathogenic fungi causing root rot disease of A. carmichaelii. This is the first report of root rot of A. carmichaelii caused by F. proliferatum.