Abstract: In order to clarify the variations in community structure and diversity of phyllosphere fungi in tobacco plants with typical infection of tobacco powdery mildew, the tobacco leaves with disease severity Ⅲ(BFn) and severity Ⅸ (BFl) were sampled from the same tobacco plant, and the fungal community structure and diversity of the samples were investigated by using Illumina high-throughput sequencing technique. The results showed that: 1) The fungal community abundance in the BFn sample were higher than that of the BFl sample. 2) At the phylum level, the dominant fungi of all the samples were Ascomycota and Basidiomycota. 3) At the genus level, BFn had more diversity than BFl. The dominant genuses of BFn were Golovinomyces (the relative abundance 99.47%), Aspergillus (0.16%), Rhodotorula (0.13%) and Alternaria (0.08%), while for BFl they were Golovinomyces (99.43%), Aspergillus (0.54%) and Alternaria (0.01%). Therefore, Golovinomyces were the dominant bacterial genus for both BFn and BFl, and its abundance was less affected by disease index.