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Nixi chicken is a type of Tibetan chickens who lives at high altitudes in China. In this study, we reported the first complete mitochondrial genome of Nixi chicken by using a next-generation sequencing method. The assembled complete mitogenome contains one control region, 2 ribosomal RNAs, 13 protein-coding genes and 22 transfer RNA genes. Our work provides a valuable source of data for the study of the evolution of the Gallus gallus mitochondrial genome and contributes to the Nixi chicken breeding improvement program.