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High-altitude Tajiks (HA-Tajiks), Tibetans and Sherpas are three groups of high-altitude native people in China. The differences in the mtDNA genome between the three populations and the role of the mtDNA genome in the high-altitude adaptation of HA-Tajiks were seldom investigated. In this study, 80 HA-Tajiks were enrolled, and their whole mtDNA genomes were sequenced. The haplogroup of each subject was determined by comparison to the revised Cambridge Reference Sequence (rCRS). Ten additional populations from East Asia and Central Asia, including Tibetans and Sherpas, were selected as references. The top haplogroup was U, followed by H, T and J. Principle component analysis and genetic distance analysis indicated that HA-Tajiks showed a close relationship with Wakhi Tajiks, Pamiri Tajiks and Sarikoli Tajiks, indicating that they should be considered one nation scattered around the Pamirs. The difference in the mtDNA genome between HA-Tajiks and Sherpas was significantly greater than that between HA-Tajiks and Tibetans. Among the 13 genes related to the OXPHOS pathway encoded by the mtDNA genome, HA-Tajiks showed more significant differences in ND3 and CYTB compared to Tibetans. Compared to Sherpas, HA-Tajiks showed more significant differences in ND1, ND2, COX1, ATP8, ATP6, ND3, ND4L, ND4, ND5 and CYTB. The associated functional changes and underlying molecular mechanisms should be explored by molecular and biochemical investigations in further studies.