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Background The sequence polymorphisms of mitochondrial DNA (mtDNA) are valuable in forensic medicine and anthropological genetics. Aim We analysed the sequences of the mtDNA control region in 207 unrelated Tibetan individuals from the Naqu region, Tibet Autonomous Region in the People's Republic of China, and investigated the population structure of the region by population comparison with other groups. Subjects and methods Genomic DNA was extracted and hypervariable regions (HVS-I and HVS-II) were amplified and sequenced. Subsequently, sequences were aligned and compared with the revised Cambridge sequence. Moreover, population comparison was performed between the Naqu Tibetan group and the other groups. Conclusion Our study provided available data for exploring the mtDNA haplotype of the Tibetan population in the Naqu region, and population comparisons found that the Naqu Tibetan population has its own unique structure.