| Summary: | The complete mitochondrial genome of the black-fin stream jewel goby Stiphodon percnopterygionus has been amplified and sequenced. The whole mitochondrial genome is 16,502 base pairs (bp) in total length and consisting of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region (CR). The overall base composition is 28.1% for A, 17.1% for G, 28.7% for C and 26.0% for T with AT comprising 54.1%. A phylogenetic tree was constructed using mitochondrial protein-coding genes (PCGs) sequence data for 34 related taxa of the order Gobiiformes showed that S. percnopterygionus is closely related to S. tuivi. These findings will contribute for phylogenetic, phylogeography and further genetic studies in genus Stiphodon and related gobiid fishes.
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