In this study, the whole mitochondrial genome sequencing of Aspergillus chevalieri, which was isolated from dark tea were analyzed and compared with its two related species (Aspergillus cristatum and Aspergillus pseudoglaucus). Results indicated that the mitochondrial genome of A. chevalieri was 56,139 bp in length, the content of the four bases A, T, C and G are 36.83%, 35.79%, 12.30% and 15.08% respectively, its genome encoded 44 genes. The phylogenetic tree constructed with mitochondrial protein‐encoding genes could effectively clarify the evolutionary relationship between A. chevalieri, A. cristatum, A. pseudoglaucus and other Aspergillus species. The morphological characteristics and extracellular enzyme activities of the 3 Aspergillus were further analyzed. Results showed that there were certain differences in the microstructure and enzymatic characteristics of the three Aspergillus species. This study improves the taxonomy status of Aspergillus and is conducive to the control of the fermentation process of dark tea. Practical applications Aspergillus is a dominant and essential microorganism in several types of fermented foods, especially dark tea. However, Aspergillus species were easy to be confused. Our research compares and analyzes the Aspergillus chevalieri, Aspergillus cristatum, and Aspergillus pseudoglaucus in dark tea from the three aspects of the mitochondrial genome, morphological characteristics, and enzyme activity, which is helpful for identify and control of the key microorganisms in the fermentation of dark tea and stabilize the product quality.