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Aspergillus luchuensis is a filamentous fungus used for food and alcohol fermentation in many Asian countries. Here, we reported the complete mitochondrial genome sequence of A. luchuensis isolated from fermented soybean brick, called as Meju, in Korea. Its mitochondrial genome was successfully assembled from raw reads sequenced using MiSeq by Velvet and GapCloser. Total length of the mitochondrial genome is 31,228 bp and encoded 44 genes (16 protein-coding genes, two rRNAs, and 26 tRNAs). Nucleotide sequence of coding region takes over 25.6%, and overall GC content is 26.4%. Phylogenetic tree of mitochondrial genomes presented A. luchuensis and Aspergillus kawachii are clustered in one clade. This mitochondrial genome can be used for further analyses of Aspergillus mitochondrial comparative genomics to improve understanding of diverse Aspergillus species.