The rare hypogean gobiid, Luciogobius pallidus, inhabits mainly in groundwater, spring, or upper rocky tidal regions in Korea and Japan. In this paper, the complete mitochondrial genome sequence of L. pallidus was firstly determined. The gene composition and order of L. pallidus were similar to most of the other fishes. The total length of the rare hypogean gobiid mitochondrial genome is 16,480 bp, including 13 protein-coding genes, 22 tRNA, 2 rRNA and 1 control region (CR). All genes were encoded on the heavy (H)-strand, with the exceptions of ND6 and eight tRNA genes, as found in other vertebrates. The CR (833 bp in length) is located between the tRNA-Pro and tRNA-Phe genes and contains three central conserved sequence blocks (CSB-D, CSB-E and CSB-F), three conserved sequence blocks (CSB-1, CBS-2 and CBS-3), and its 3' end embeds a poly-T-nucleotide sequence.
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