In this study, the complete mitochondrial genome of a male individual of Murina cyclotis from Guangxi province, China, was sequenced and analyzed. The genome is a circular molecule of 16,463 bp length, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. Most of the genes were encoded on the H-strand, except for 8 tRNA and ND6 genes. Phylogenetic trees of the complete mitochondrial genome were constructed using RAxML. Our result suggests that M. cyclotis is closely related to M. leucogaster from Korea. The complete mitochondrial genome sequence of M. cyclotis will be helpful for future taxonomic and phylogenetic studies on Murina.