The microfungal population structure of two Scots pine forest soils in Southern Sweden was studied 8–13 yr after nitrogen fertilization. The different fertilizers used. ammonium nitrate and urea. influenced the species composition in different ways. The main effect of the NH4NO3 treatment was an increased isolation frequency of Penicillium spinulosum and 4Oidiodendron echinulatum, while Penicillium cf. brevi-compactum. Mortierella subgenus Mortierella. Chaunopycnis alba and Oidiodendron griseum were isolated less frequently in ammonium nitrate-amended treatments compared to the non-fertilized control. In the urea-fertilized plots the isolation frequency of P. cf. brevi-compactum increased, while that of C. alba. O. echinulatum, O. griseum and P. spinulosum decreased in comparison with control plots. The changes in species composition were most evident at the highest rate of application, 600 kg N ha−1, especially when NH4NO3 was used as a fertilizer.