Here, we report the complete mitochondrial genome of a Bombyx mori strain BaiyuN, which is identified to be highly resistant to Bombyx mori nucleopolyhedrovirus (BmNPV). Its complete mitochondrial genome is 15,655 bp in length (GenBank accession no. MG797555), consisting of 13 protein-coding genes, 22 tRNA genes, 2 rRNA, and 1 control region (494 bp). The complete mitogenome of the B. mori strain BaiyuN could provide a basic data for further phylogenetics and antivirus research.