[Objective] Shallot Fusarium rot disease occurred constantly during storage. It was important for controlling the disease to confirm the pathogenic Fusarium species of the disease. [Methods] The pathogens of shallot storage Fusarium rot disease were isolated and cultured purely by tissue isolation method from 16 samples collected from Lanzhou markets in Gansu province, China. The generated Fusarium strains were identified by morphological characteristics and analysis of rDNA-ITS, EF-1a(tef) gene sequences after single spore isolation. [Results] The generated 80 Fusarium strains belonged to three species including F. proliferatum, F. oxysporum and F. avenaceum. F. proliferatum with 52.50 percentage isolation frequencies was the dominant pathogen of shallot Fusarium rot disease. The pathogenicity test showed that the pathogenicity of F. proliferatum was the strongest in shallot bulbs among the three Fusarium species, F. avenaceum was the weakest. [Conclusion] Three pathogenic Fusarium species were firstly reported as the pathogens of shallot storage Fusarium rot disease in Ganshu province, China.