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Gymnopilus junonius, a well-known poisonous mushroom, is distributed worldwide. It contains a hallucinogenic alkaloid psilocybin and several other bioactive compounds. The mitochondrial genome, a circular DNA molecule of 161,145 bp, comprises 15 protein-coding genes, 24 transfer RNA genes, and 2 ribosomal RNA genes. The guanine-cytosine content was 31.56%. Based on the mitochondrial genome sequence, a phylogenetic tree was constructed to demonstrate the phylogenetic relationship. In this study, the phylogenetic positions of G. junonius and its related genera were determined.