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We sequenced the mitochondrial genome of a rare Chinese stag beetle Kirchnerius guangxii using the next-generation sequencing. The mitochondrial genome is 14,562 bp in length, containing 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs) and 22 transfer RNA genes (tRNAs). The phylogenetic analyses showed that K. guangxii was sister to the clade of Epidorcus gracilis and Serrognathus platymelus, and had a relatively low genomic affinity to Prosopocoilus. Thus, K. guangxii had a more close relationship with Epidorcus, Serrognathus and Dorcus than Prosopocoilus, which was different from previous morphological study. Our result can provide more available mitogenomic data for discussing the phylogeny of Kirchnerius and facilitate the phylogenomic research of the family Lucanidae.