Here, we report a metabarcoding (ITS2) study to define the common core fungal microbiome (mycobiome) of healthy Musa spp. (bananas and plantains). We conducted a meta-analysis of eleven publicly available datasets of Musa spp. associated fungi demonstrating that the core fungi identified in our study have close relatives in other countries. The diversity and composition of mycobiomes differed between plant compartments and soils, but not genotypes. The core mycobiome included Fusarium oxysporum and its relatives, which dominated all plant compartments, as well as members of the Sordariomycetes, Dothideomycetes, and Mortierellomycota. Our study provides a robust list of common core fungal taxa for Musa spp.