Soil fungi and oomycetes (syn. peronosporomycetes) are the most common causes of pea diseases, and these pathogens often occur in complexes involving several species. Information on the dynamics within this complex of pathogens, and also between the complex of pathogens and other fungi in the development of root disease is limited. In this study, next-generation sequencing of nuclear ribosomal internal transcribed spacer-1 was used to characterize fungal communities in agricultural soils from nine pea fields, in which pea roots showed different degrees of disease. Fungal species richness, diversity, and community composition were analyzed and compared among the different pea soils. After filtering for quality and excluding non-fungal sequences, 55,460 sequences clustering into 434 operational taxonomic units (OTUs), were obtained from the nine soil samples. These sequences were found to correspond to 145–200 OTUs in each soil. The fungal communities in the nine soils were strongly dominated by Ascom