Background: The intestinal microbiota play remarkable roles in maintaining the health of their hosts. Recent studies focused on gut bacterial diversity in birds and poultry, with little information about the ecological functions of their gut fungal community.Methods: The high-throughput sequencing was applied to compare intestinal fungal community structure between Hooded Crane (Grus monacha) and Domestic Goose (Anser anser domesticus), and infer the potential pathogens of each species at Shengjin Lake of China. Results: Intestinal fungal alpha diversity was higher in Hooded Crane than Greylag Goose (Anser anser). Gut fungal community composition showed dramatic shifts between the two species. Hooded Cranes mainly eat Vallisneria natans and Potamogeton malaianus, while artificial hurl food (i.e., paddy) was the main food resource for Domestic Geese, suggesting that the variations in fungal community might be induced by different diets between the two hosts. Two enriched genera (i.e., Acremonium and Rhodotorula) which could increase host's digestion were detected in guts of Hooded Cranes. In addition, there were 42 pathogenic amplicon sequence variants (ASVs), 17％ of which shared in Hooded Crane and Greylag Goose. The Hooded Crane had higher gut fungal pathogenic diversity and abundance relative to Greylag Goose. Conclusions: The study demonstrated that divergence in intestinal fungal community structure might be induced by different diets between wintering Hooded Crane and Domestic Goose. Hooded Crane might rely more on their gut fungal taxa to acquire nutrients from indigestible food resources. Our study also implied that more research should focus on intestinal pathogens in wild birds and domestic poultry, as they might increase risk of disease in other animals, even human beings. The degree of cross infection in pathogens among wild birds and sympatric poul-try should be clearly verified in future study.