The greenfin horse-faced filefish, Thamnaconus septentrionalis, is a valuable commercial fish that is widely distributed in the Indo-West Pacific Ocean. It has characteristic blue-green fins, rough skin and spine-like first dorsal fin. T. septentrionalis is of a conservation concern as a result of sharply population decline, and it is an important marine aquaculture fish species in China. The genomic resources for T. septentrionalis are lacking and no reference genome has been released.