Amazonian Dark Earth (ADE) is a highly fertile anthropogenic origin soil characterized by higher amounts of charred black carbon (BC). ADE is considered a fertility model, however few information about the microbial communities structure and diversity inhibiting ADE and BC and the effects of land use in the communities is available. Fungal community structure and diversity of ADE and BC from four sites under different land uses (three agricultural systems and a secondary pristine forest) in the Brazilian Central Amazon was evaluated by 18S rRNA gene pyrosequencing. Fungal communities in the ADE and BC were dissimilar and showed differential abundances of fungal Operational Taxonomic Units (OTUs). Estimated fungal species richness (ACE and Chao-1) and diversity (Shannon and Simpson’s reciprocal) indices were higher in the ADE than in the BC under agricultural use. No significant differences were observed in the same estimators in the ADE and BC samples under secondary forest, suggesting an effect of land use on the fungal communities. Furthermore, shifts in the fungal communities due to land use were observed by the dominance of Pezizomycotina fungi in the ADE areas under agricultural use and Agaricomycotina in the ADE under secondary forest. The BC particles were dominated by Pezizomycotina fungi, and OTUs assigned to Cordyceps confragosa, Acremonium vitellinum, Camarops microspora and Hirsutella rhossiliensis were more abundant than in the ADE. This study is a breakthrough in the understanding of fungal communities in ADE and BC and can also be valuable in the future studies considering biochar application in soil.