This archive contains the sequencing data we used to characterizing the soil fungal microbiomes in the University of Minnesota Cedar Creek BigBio enemy removal experiment. For this project, we sampled soil microbiomes from control and foliar fungicide plots in both monoculture and 16 species polyculture at 2013 and 2014. All sequencing data is compressed in a single file for 2013 data. For 2014 data, samples are sequenced on two MiSeq runs. Read1 and Read2 sequences are saved in four compressed files (two for each run).