This sequence dataset (FASTQ format) was obtained by metabarcoding fungal communities of 20-days old leaves in an untreated vineyard located in INRA Vilenave d'Ornon (France). The ribosomal internal transcribed spacer region 1 (ITS1) was amplified with the ITS1F / ITS2 primer pair and sequenced on an Illumina MiSeq platform (v2 chemistry, 500 cycles). "M" samples were collected from leaves harboring symptoms of powdery mildew (Erysiphe necator), while "S" samples were collected from visually healthy leaves. "ZI" samples correspond to disease spots and "ZS" samples were taken from the healthy leaf blade of infected leaves. The "info_16S" caption is misleading, the sequences are fungal ITS sequences.