Arbuscular mycorrhizal (AM) fungi improve the uptake of phosphate from soil through symbiotic associations with plant roots. The introduction of winter crops has been shown to increase nutrient uptake and yield of subsequent crops, and may result from increased AM fungal biomass in the soil. However, there is little information regarding the effects of different winter crops on AM fungal communities in soil. The present study evaluated the impact of various winter crops on AM fungal species composition in the soils. A three years field experiment was conducted at Nihon University in Kanagawa, Japan. Replicated plots of winter sown wheat, spring sown wheat, canola and fallow were established in 2007, and wheat, red clover, canola and fallow were established in 2008 and 2009. Before the winter crop, soybean as summer crop was sown in all plots. The AM fungal species composition in soils was determined using nested PCR and partial LSU rDNA primers and was characterized by each clone library of partial LSU rDNA sequencing. By RDA (Redundancy analysis), the winter crops did not have any effects on the AM fungal communities in the soils in 2007 and 2008. Moreover, there was not significant difference between the AM fungal species composition in each soil by a Monte Carlo 999 permutations test. However, the winter crops have a strong effect on the AM fungal communities in the soils in 2009. In addition, there was significant difference between the AM fungal species composition in each soil by a Monte Carlo 999 permutations test. Thus, continuous rotation of winter and summer crop has the potential to change the species composition of AM fungal communities in soil.