Amazonian Dark Earth (ADE) is a highly fertile soil of anthropogenic origin characterized by higher amount of charred black carbon (BC). ADE is considered a fertility model, however knowledge about the fungal community structure and diversity inhabiting ADE and BC is scarce. Fungal community structure and diversity of ADE and BC from four sites under different land use (three agricultural systems and a secondary pristine forest) in the Brazilian Central Amazon was evaluated by 18S rRNA gene pyrosequencing. Fungal communities in 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 ADE than BC in all agricultural areas. No differences were observed in the same estimators in ADE and BC samples under secondary forest. Pezizomycotina fungi, and OTUs assigned to Cordyceps confragosa, Acremonium vitellinum, Camarops microspora and Hirsutella rhossiliensis were more abundant in BC particles than in ADE. This study is a breakthrough in understanding the fungal communities in BC particles from ADE and can also be valuable in future studies considering biochar application in soil.