Fungi living in and around potato roots and leaves influence nutrient uptake and dis-ease, yet the mycobiome of potato cultivars grown in the Andes, the crop’s centre of diversity, remains almost undescribed. We characterised fungal communities (ITS2 metabarcoding, Illumina MiSeq) in the rhizosphere soil and in surface-sterilised roots and leaves of two improved cultivars (INIAP-Gabriela and Superchola) and one native cultivar (Pan de Azúcar) grown in a smallholder field in Chimborazo, Ecuador. All 24 libraries were processed with a single pipeline, yielding 479,635 fungal reads and 398 amplicon sequence variants (ASVs). Diversity fell stepwise from rhizosphere to roots to leaves (median 98, 18 and 8 ASVs at equal depth; Kruskal–Wallis p < 0.001), and compartment was the main driver of community structure (PERMANOVA R² = 0.196, p = 0.001; roots vs. leaves R² = 0.094, p = 0.041). Cultivar had no significant effect in the rhizosphere (R² = 0.422, p = 0.343), roots (R² = 0.305, p = 0.157) or leaves (R² = 0.342, p = 0.149). The rhizosphere was dominated by Mortierellaceae (10–34%), Mucor (5–14%), Cladosporium and Tremellomycetes yeasts. Most endophytic reads came from ASVs also present in the rhizosphere (65% in roots, 81% in leaves), and five of the seven core endophytic genera (Mucor, Cystofilobasidium, Candida, Naganishia and Leucosporidium) occurred in soil. Entry into the plant was selective: Mortierellaceae fell to < 1% of root reads and were absent from leaves, Nectriaceae (Gibberella), Cladosporium and Didy-mellaceae were nearly excluded, whereas Olpidium and Naganishia were enriched in roots and the black yeast Exophiala in leaves (DESeq2, padj < 0.05). The endophytic mycobiome was dominated by cold-tolerant basidiomycetous and ascomycetous yeasts. These results show a stepwise filtering of the soil mycobiome from rhizosphere to leaf and nominate core fungi for culture-based screening of locally adapted bioinputs.