Abstract: Eichhornia crassipes has become one of the most serious malignant aquatic weeds in recent years due to its separation from the restriction of natural enemies and natural factors, in addition to its extremely strong ability to reproduce and spread. The use of biological control method to control Eichhornia crassipes is recognized as a safe and effective method at home and abroad. Eichhornia crassipes has been introduced in Quanzhou for several decades, and it may produce microbial natural enemies in the adaptation process of Eichhornia crassipes. The disease investigation of Eichhornia crassipes was carried out in the agricultural science and technology park of Quanzhou Institute of Agricultural Sciences. It was found that the leaf blight of Eichhornia crassipes was the most obvious in the water area, which could cause the large area of Eichhornia crassipes leaves to wilt. Two pathogenic fungi causing the leaf blight of Eichhornia crassipes were isolated and obtained by means of isolation, purification and identification of pathogenic fungi. Combined with the morphological analysis of strains and ITS sequence analysis, they were identified as Alternaria alternata YQ21 and Alternaria brassicicola YQ36. Alternaria brassicicola YQ36 was the first discovered pathogen of Eichhornia crassipes in Fujian Province, which enriched the resource library of natural enemy microorganisms of Eichhornia crassipes in Fujian Province.