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The complete mitochondrial genome (mitogenome) sequence of Sphenomorphus incognitus was determined by shotgun sequencing. The total length of mitogenome is 17 417 bp, and contains 13 protein-coding genes, 22 tRNA genes, two ribosome RNA genes and two non-coding regions (the control region and the putative L-strand replication origin). Most of the genes of S. incognitus were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand. The phylogenetic tree of S. incognitus and 8 other closely species was built. The DNA data presented here will be useful to study the evolutionary relationships and genetic diversity of S. incognitus.