Aspergillus luchuensis is a filamentous fungus used for food and alcohol fermentation in many Asian countries. Aspergillus parasiticus is a notorious filamentous fungus, which can produce aflatoxin B and G. And Aspergillus pseudoglaucus is a xerophilic filamentous fungus which can produce various secondary metabolites. Here, we reported the complete mitochondrial genome sequences of A. luchuensis and A. pseudoglaucus isolated from fermented soybean brick, called as Meju, in Korea, and A. parasiticus also isolated in Korea. The mitochondrial genomes were successfully assembled from raw reads sequenced using MiSeq by Velvet and GapCloser. Total length of the A. luchuensis, A. parasiticus and A. pseudoglaucus mitochondrial genomes are 31,228 bp and encoded 44 genes (16 protein-coding genes, two rRNAs, and 26 tRNAs), 29,141 bp and encoded 45 genes (17 protein-coding genes, 2 rRNAs, and 26 tRNAs), and 53,882 bp, which is third longest among known Aspergillus mitochondrial genomes and encoded 58 genes (30 protein-coding genes including hypothetical ORFs, two rRNAs, and 26 tRNAs), respectively. The mitochondrial genomes can be used for further analyses of Aspergillus mitochondrial comparative genomics to improve understanding of diverse Aspergillus species.