Abstract: In order to investigate the genetic differentiation of domestic sika deer in Jilin Province, the complete mitochondrial mtDNA Cytb gene was sequenced by DNA direct sequencing technology. The obtained sequences were analyzed based on the homologous sequences of other sika deer subspecies published in GenBank by using biology software. A total of 38 polymorphic sites were found in the mtDNA Cytb gene sequences from 15 sika deer. The analysis results showed that the genetic diversity of domestic sika deer in Jilin Province was relatively low. The domestic sika deer in Jilin Province was genetically closely related to the subspecies in Russia, Korea and North Korea. However, it has a distant relationship to subspecies in Sichuan Province.