Abstract: Qingyuan partridge chicken, as one of the famous native chicken（Gallus gallus gallus） breeds in China, has undergone systematical conservation and utilization for 20 years, nevertheless its core conservation population lacks genetic diversity evaluation. In this study, a total of 99 mitochondrial genome from the breeding population and conservation population of Qingyuan partridge chickens were determined by high-throughput sequencing. On this basis, this study conducted a comprehensive evaluation on the genetic diversity level of the mitochondrial genome of Qingyuan partridge chicken. It was found that the genetic diversity of its mitochondrial genome was relatively high. All non-coding genes as well as coding genes including COⅠ, ND4, COⅢ, ND2 and Cytb had high level of ave-rage number of nucleotide differences（K）, indicating that Qingyuan partridge chicken had a good effect on breed conservation. The results also showed that the conservation population had higher genetic diversity than breeding populations. Meanwhile, conservation population had higher gene haplotype diversity（H_d） than breeding populations for all coding genes except for ND1 and COⅡ. The sequence alignment results of mitochondrial genome coding regions between two populations showed that, a total of 30 missense mutations were identified among the breeding populations, including two radical mutations in ND3 and ND5 genes, respectively, while a total of 24 missense mutations happened among the conservation population, including one moderate radical mutation in COⅢ and one radical mutation in ND3, suggesting that Qingyuan partridge chicken had great breeding potential. In summary, this study provided a theoretical reference for the protection, evaluation and rational utilization of Qingyuan partridge chickens.