The difference of arbuscular mycorrhizal fungi community structure infected in roots between crops or regions was clarified. It is the crop in which corn and soybean sampled the root. The sampling of the crop roots was carried out at 5 Prefectures (Hokkaido, Kanagawa, Yamanashi, Yamaguchi and Fukuoka). The roots of both crops were collected from adjoining field. There was a difference in the community structure of infected arbuscular mycorrhizal fungi between crops. Concretely, AM fungi community structure that infected in the soybean roots was more various than that of maize roots. Glomus intraradices was peculiarly infected in maize roots. This tendency also applied to the crop roots collected in all Prefectures. It is indicated that the host affinity exists arbuscular mycorrhizal fungi and host plants. The infection ratio of arbuscular mycorrhizal fungi collected in Kanagawa, Yamanashi were higher than that in other Prefectures. However, the community structure of arbuscular mycorrhizal fungi were also not always various in the plants in which infection ratio were higher. It was considered that there was large difference in the community structure of arbuscular mycorrhizal fungi, which infects the root between regions.