Amazonian Dark Earth(ADE) is a highly fertile soil of anthropogenic origin characterized by high levels of charred black carbon(BC). It is considered a model of fertility; however, knowledge on the fungal community structure and diversity inhabiting ADE and its BC particles is scarce. Fungal community structure and diversity of ADE and its BC from four sites under different land uses(three agricultural systems and a secondary pristine forest) in the Brazilian Central Amazon were 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(abundance-based coverage estimate and Chao-1 index) and diversity estimators(Shannon and Simpson’s reciprocal indices) were higher in ADE than in BC in all agricultural areas. No differences were observed in those parameters in ADE and BC samples from the 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. These findings represent a breakthrough in our understanding of fungal communities in BC particles from ADE, and will be valuable in future studies considering biochar application in soil. Amazonian Dark Earth (ADE) is a highly fertile soil of anthropogenic origin characterized by high levels of charred black carbon (BC). It is considered a model of fertility; however, knowledge on the fungal community structure and diversity inhabiting ADE and its BC particles is scarce. Fungal community structure and diversity of ADE and its BC from four sites under different land uses (three agricultural systems and a secondary pristine forest) in the Brazilian Central Amazon who 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 (abundance-based coverage estimate and Chao-1 index) and diversity estimators (Shannon and Simpson’s reciprocal indices) were higher in ADE than in BC in all agricultural areas. No differences were observed in those parameters in ADE and BC samples from the secondary forest. Pezizomycotina fungi and OTUs assign ed to Cordyceps confragosa, Acremonium vitellinum, Camarops microspora, and Hirsutella rhossiliensis were more abundant in BC particles than in ADE. These findings represent a breakthrough in ADA, and will be valuable in future studies considering biochar application in soil.