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The toad-headed lizards of genus Phrynocephalus are one of the most prevalent animals in the central Asian desert. A few studies have investigated molecular phylogenesis of Phrynocephalus, yet yield inconsistent results. Moreover, these studies were only based on a few specific DNA fragments of mitochondrial genome. To facilitate the clarification of molecular phylogenesis of Phrynocephalus, we conducted this study to sequence the entire mitochondrial genome of the Phrynocephalus helioscopus collected from Northwest China. The length of complete mitochondrial DNA is 16,249 nucleotides, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 control regions (CR). The gene arrangement and composition of P. helioscopus resemble those of other Phrynocephalus sand lizard, except for P. przewalskii and P. versicolor. The overall A, T, C, G base composition of the heavy-strand was 35.9%, 26.4%, 25.2%, 12.5%, respectively, which is biased toward AT (about 62.3%). The AT-biased base composition was similar to what observed in most vertebrates. The complete mitochondrial genome of P. helioscopus may help to clarify the phylogenetic relationships related to Phrynocephalus oviparity.