Abstract: Aimed to lay references for the whole genome sequencing and provide basic data for the genetic relationships between Bombyx mandarina and Bombyx mori, the genome of Bombyx mandarina was investigated and the mitochondrial genome was analyzed. Using the Illumina Hiseq 2500 pair-end sequencing platform, a female Bombyx mandarina was sequenced, the genome size, heterozygosity and GC contend have been estimated based on the genomic survey analysis, and the genome of wild silkworm has been pre-assembled. Using the sequencing data, the mitochondrial genome sequences in the genome were extracted and assembled directly. As results, 25.8 GB clean data was obtained, the estimated genome size of Bombyx mandarina was 456.5 Mb, the heterozygosity rate was 1.94%. After preliminary assembly, the scaffold N50 was 1 792 bp, scaffold number was 737 055, contig N50 was 587 bp, contig number was 1 477 268. As assemblyand annotation, the mitochondrial genome of wild silkworm was 15 662 bp, a total of37 genes were arranged in the mitochondrial genome, which did not have a gene rearrangement. According the phylogenetic tree of mitochondrial genome, wild silkworm could be divided into north or south group according to the geographical source. Subgroup of Wild silkworm from the North China had the closest genetical relationship with the domestic silkworm. Since the genome of Qin-ba wild silkworm belonged to the complex genome, integrating the second, the third generation sequencing and Hi-C technology could be helpful to obtain high quality genomic of Bombyx mandarina. This study also supported the contention that domestic of silkworm descended from the Northern of China, and implied that the Qin-ba mountain area could be one of the original regions of domestic silkworm.