Deforestation of the Atlantic rainforest in Brazil and its conversion into sugarcane fields, pose a serious threat to the local biodiversity. The change in land use affects not only macro-organisms, but also microbial communities such as the obligate symbiotic arbuscular mycorrhizal fungi (AMF). We characterized AMF communities along 200-m transects from native forests and into sugarcane fields. Meta-barcoding, and subsequent community and network analyses were used to illustrate the distribution of communities along the transects. Conversion of forest into sugarcane fields did not change alpha diversity, but resulted in a biotic homogenization of the communities. The communities in the sugarcane field was not a subset of the forest community, but recruited taxa from other unsampled species pools. We found a peak in richness in the transition zones which suggests that the AMF community admix across the border. A difference in nestedness and high turnover among transects indicate that forest AMF are locally specialized and have a restricted geographical range.