Intestinal fungi are an important component of the microbiota, and recent studies have unveiled their potential in modulating host immune homeostasis and inflammatory disease. Nonetheless, the mechanisms governing immunity to gut mycobiota remain unknown. We identified CX3CR1+ mononuclear phagocytes (MNPs) as essential for the initiation of innate and adaptive immune responses to intestinal fungi. Genetic ablation of CX3CR1+ MNPs led to changes in the gut fungal communities. Cx3cr1DTR mice were bred to hemizygous Cd11c-cre+/- mice (expression of Cd11c-cre excises the floxed stop cassette, allowing for DTR expression in CD11c+ cells) to allow for selective depletion of CD11c+ CD11b+ CX3CR1+ MNPs upon administration of diphtheria toxin (DT). For depletion, mice generated through such breeding (Cd11c-cre+/- Cx3cr1DTR mice) and the respective littermate controls (Cd11c-cre-/- Cx3cr1DTR) were injected for three consecutive days with 100ng of DT i.p followed by maintenance injection every other day for 7 days prior to feces collection.