We sampled 16 soil cores along a 270 cm transect in a meadow to characterize the fungal communities. Amplicons have been sequenced on a Illumina MiSeq platform. Deposited files contain demultiplexed reads (both forward and reverse in 5'-3' direction). File names correspond to three annealing temperatures (52,55 and 58°C), PCR replicates (1-3) and sample numbers (1-16) (annealing_PCR_sample).