Bat populations are highly diverse, making bat species taxonomy and phylogenetic relationships an important research topic. Mitochondrial DNA, a form of maternal inheritance, has been extensively used in species relationship research. Barbastella caspica has spread widely in the Caspian region, Iran, and Central Asia, however there is no evidence of its occurrence in China. During a field investigation, we obtained a single specimen of the B. caspica species for the first time in China’s Xinjiang Uyghur Autonomous Region. We sequenced the entire mitochondrial genome, presented its genomic structure and features, and examined its evolutionary position in relation to its congenerous. The mitochondrial genome of B. caspica spans 16,933 bp, composing 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a displacement loop/control region. Consistent with previous bat mitogenome reports, the majority of mitochondrial genes are encoded on the heavy chain. With the exception of the DHU arm in tRNA-Ser1, all other tRNAs exhibit a “cloverleaf” secondary structure. Phylogenetic analysis based on 13 protein-coding genes revealed that Rhogeessa, Plecotus, and B. caspica formed one clade within the Vespertilionidae. B. caspica was found to be a sister species to B. beijingensis and B. leucomelas in the phylogenetic trees using the cytochrome b and ND1 gene sequences, respectively. This is the first report of the Barbastella genus’ mitogenome, as well as the first record of a B. caspica species from China.