Despite extensive research on the gut bacteriome during infancy and its correlation with various chronic diseases, the influence of diet on gut mycobiome development in infants remains unexplored. To address this significant research gap, we conducted a study on 70 healthy Hong Kong Chinese infants who were either directly breastfed, expressed milk-fed, or formula-fed. Our analysis revealed that formula-fed infants had higher fungal diversity and composition in their gut mycobiome compared to those in breastfed and expressed milk-fed infants. The formula-fed group exhibited higher fungal richness, with a median of 58.5, compared to a median of 34 in the breastfed group (