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Phytopathogenic fungi are a major cause of plant disease. However, the interrelationships between phytopathogenic and non-phytopathogenic fungi in the peanut (Arachis hypogaea) monoculture system remain unclear. In this study, rhizosphere soils from four fields that had been monocropped with peanut for different durations were investigated, including monoculture for 1 year (CK), 4 years (P4), 10 years (P10), and 20 years (P20). Illumina sequencing of fungal ITS regions and FUNGuild were used to investigate the interrelationships between potential phytopathogenic and non-phytopathogenic fungi. Our results showed that the relative abundance of potential phytopathogenic fungi was significantly negatively correlated with that of non-phytopathogenic fungi (r = −0.650, P = 0.022); and the relative abundance of the key potential phytopathogenic species, Fusarium, was also significantly negatively correlated …