Little is known about the responses of soil fungal communities to revegetation of mine wastelands, representing a major gap in the knowledge needed to improve the performances of revegetation schemes for mine wastelands. To shed some light on this matter, we re-established 4000 m² of vegetation on an extremely acidic (pH 2.5) copper mine tailings pond and collected soil samples from three different types of habitats: amended layer of the reclaimed tailings (ALRT), unamended layer of the reclaimed tailings (ULRT), and unreclaimed tailings (UT). Soil fungal communities in the 120 samples collected in two consecutive years were characterized via high-throughput sequencing. The fungal diversities at ALRT and ULRT were found to be significantly higher than those at UT. Ascomycota whose relative abundance ranged from 74.5% to 98.4% was the most predominant phylum across all habitats, exhibiting the lowest predominance at ALRT. Two acidophilic fungal genera, Acidomyces and Acidiella, dominated UT with relative abundances being as high as 37.8% and 15.2%, respectively. In contrast, three genera with plant growth-promoting species (Talaromyces, Trichoderma and Penicillium) were abundant at ULRT and ALRT. Remarkably, their relative abundances at ULRT could be up to 29.0%, 26.9% and 9.7%, respectively. The three types of habitats differed considerably in the overall soil fungal community composition at species level, which became more pronounced as time progressed. The abovementioned differences between habitats in soil fungal community features were related to the reduced availability of soil copper and zinc. These results improved our understanding of fungal ecology of mine wastelands.