background and aims: Arbuscular mycorrhizal (AM) fungi play a significant role in P nutrition of crops in agriculture, but P accumulation in soil, e.g., application of P-fertilizer, generally reduces AM fungal colonization. The impact of long-term application of chemical fertilizer on AM fungal communities was investigated with respect to the time scale. Methods: Soils were collected from four plots with different fertilizer management in the long-term experimental fiels established in 1914. Lotus japonicus was grown in the soils in a greenhouse, while Glycine max was grown in the plots in the field. DNA was extracted from their roots, and the diversity and the community compositions were analysed based on occurrence of the AM fungal phylotypes defined by sequence similarity in the LSU rDNA. Results: The 90-year application of N and K in the absence of P increased AM fungal diversity and resulted in formation of a distinctive fungal community compared withthose in the other treatments. This effect was not cancelled by single application of P. Whereas the impact of balanced application of N,P and K was ambiguous. Conclusion: These observations suggest that the presence/absence of P-fertilizer has a major impact on AM fungal communities, but the action may appear only on a long time scale.