Gymnocypris przewalskii kelukehuensis: (Teleostei: Cyprinidae) is a new subspecies of Gymnocypris przewalskii which endemic to Lake Keluke on the Tibetan Plateau,. However, it is now threatened by exotic species invasions and overfishing, and its natural population has been dramatically decreased. Here we firstly report its complete mitochondrial genome by low-coverage whole genome sequencing method. The total length of mitogenome is 16,682 bp, including 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs) and two ribosomal RNAs (rRNAs). The putative control region is located between tRNA-Phe and tRNA-Pro, with an A + T content of 64.11%. The base composition of the genome is A (28.73%), C (25.86%), G (18.04%) and C (27.35%) with an overall GC content of 43.91%. Phylogenetic analysis suggests that G. p. kelukehuensis is closely related to G. przewalskii complex.