Fungi play an important role in bioremediation of contaminated soil. However, the diversity of fungal populations in four mine-contaminated soils located in Hechi City has remained unexplored. In this study, high-throughput sequencing of ITS was performed to investigate the diversity and abundance of fungal communities in four mine-contaminated soils in Hechi city. Phylogenetic taxonomy showed that the fungal communities included five phyla.AscomycotaandBasidiomycotawere the most abundant phyla in four samples. The most abundant fungi includedAgaricomycetes,Nectriaceae,Eurotiomycetes,Mortierellaceae,Incertae sedis,Trichocomaceae,Sordariomycetes, andFusarium. Various fungi with the potential of bioremediation and industrial application were discussed. The results of fungal composition will provide a clue for isolation of new fungi with the potential of bioremediation and industrial application. Furthermore, this study will lay a good foundation for modifying the indigenous fungi by genetic engineering in the future.