The mitogenome of the Hypsugo alaschanicus is a circular module of 16,911 bp, which consists of 37 genes, containing 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes (12S rRNA and 16S rRNA), and a control region. The mitogenome of H. alaschanicus is AT-biased, with a nucleotide composition of 33.9% A, 30.8% T, 22.5% C, and 12.8% G. The phylogenetic analysis revealed that two Korean H. alaschanicus individuals were well grouped and formed a sister to the Chinese individual.