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• Corn yield was closely coupled with soil fungal abundance and diversity. • Mineral and organic fertilization led to divergence in fungal communities. • Soil fungal community composition was primarily driven by SOC content. Fertilization maintains soil fertility and maximizes crop productivity, but changes soil microbial community structure and functions. However, little is known about the effects of long-term mineral and/or organic fertilization on fungal communities which regulate nutrient cycling and crop growth. The responses of fungal abundance and community structure to 29-year mineral and/or organic fertilization were investigated in Ultisol using quantitative polymerase chain reaction (qPCR) and high-throughput sequencing (Illumina Mi-Seq). Compared to the control, mineral N fertilization decreased fungal abundance by 44%, but showed little effect on crop yield and fungal diversity. The NPK fertilization increased crop yield by 4.5 times and fungal diversity by 1.4 times, but had little effect on fungal abundance relative to the control. Manure application increased crop yield by 8.4 times, fungal abundance by 1.8 times and fungal diversity by 1.5 times relative to the control. Application of manure plus NPK increased crop yield by 9.5 times, fungal abundance by 1.9 times and fungal diversity by 1.6 times relative to the control. Long-term fertilization led to dramatic shifts in fungal community composition. Compared to the control, mineral and organic fertilization decreased the relative abundance of Ascomycota and Basidiomycota, respectively. The fungal community composition diverged between soils with mineral and organic fertilization. Changes in soil organic carbon (SOC) and nutrient contents primarily shifted fungal abundance and community structure. Manure application resulted in higher SOC and nutrient contents, and thus affected fungal abundance and community structure more strongly than mineral fertilization. Manure application rather than mineral fertilization increased the relative abundance of certain favorable fungal taxa (e.g., Pseudaleuria and Hypocreales) which suppress crop pathogens. Overall, long-term manure application explained patterns in soil fertility, crop productivity, fungal abundance, diversity and community composition better than mineral fertilization. [ABSTRACT FROM AUTHOR]