The complete mitochondrial genome was sequenced from the toad-headed viviparous lizard subspecies, Phrynocephalus erythrurus parva, which occupies the highest regions of any reptile on the earth. The mitogenome sequence was 16,431 bp in size, with the overall base composition of H-strand is T: 26.06%, C: 25.14%, A: 36.45%, G: 12.35%. It consists of 13 protein coding, 22 tRNA, 2 rRNA genes and 3 control regions, and its gene order and gene content were identical with the published congeneric mitogenomes of other Phrynocephalus, except for the small protion between tRNA-Pro and tRNA-Phe.