To assess the importance of arbuscular mycorrhizal fungi (AMF) to crop production, it is crucial to introduce cover crops during winter to increase growth and yield of subsequent crops. We investigated the impact of winter cover crops, on AMF communities colonizing the roots of subsequent soybean in five-years of consecutive soybean (Glycine max (L.) Merr.) rotational systems cropped to wheat (Triticum aestivum L.), red clover (Trifolium pratense L.), rapeseed (Brassica napus L.) or left fallow, respectively. Phylogenetic analysis revealed that 22 AMF phylotypes, including 11 Glomus, three Gigaspora, two Scutellospora, three Acaulospora, one of each Diversispora, Paraglomus and unknown glomeromycete in the roots. The five-years rotation with winter cover crops did not impact molecular diversity of AMF communities colonizing the roots of soybean. In all of the rotations, Glomus and Gigasporaphylotypes was common to in the roots over the five-year period. Redundancy analysis (RDA) demonstrated that AMF communities in the roots of subsequent soybean were not significantly different among winter cover crop rotations or fallow. However, AMF communities in soybean roots were clearly influenced by rotation year suggesting that climate or other environmental factors were more important than winter cropping system management.