A number of species in are important plant pathogens. Due to a limited number of synapomorphic characters, it is difficult to perform species identification and to estimate phylogeny of based solely on morphology. In this study, we sequenced the complete mitochondrial genome of , and presented the detailed annotation of the genome. The mitochondrial genome is 137,775 bp long, and contains two ribosomal RNA genes, 12 core protein-coding genes, 38 tRNA genes. In addition, two ribosomal protein genes ( gene and gene) and the fungal mitochondrial RNase P gene () are identified. The large genome size is mostly determined by the presence of numerous intronic and intergenic regions. A total of 28 introns are inserted in eight core protein-coding genes. Together with the published mitochondrial genome sequences, we conducted a preliminary phylogenetic inference of Dothideomycetes under various datasets and substitution models. The monophyly of , and are consistently supported in all analyses. The forms an independent lineage, with a distant phylogenetic relationship to . At the family level, the , . , and are recognized in the majority of trees.