Species of the family Scorpaenidae are easily misidentified due to their similar appearances, a result of camouflaging to their surroundings. In recent years, many species from this family have been described, and generic placements of some species have been revised. Previously, there were 80 species belonging to 29 genera of the Scorpaenidae recorded in Taiwanese waters. However, their taxonomy has not been revised for decades. It is necessary to update the checklist of the Scorpaenidae occurring in Taiwanese waters based on updated morphological and molecular data. In the present study, we revised the Taiwanese scorpaenids based on 296 specimens and updated the checklist, amounting to a total of 85 species of 29 genera, of which Sebastapistes mauritiana (Cuvier) is a new record, and three species from the genera Phenacoscorpius, Scorpaenopsis, and Sebastapistes are unable to be identified to any species. Using molecular analysis, we conducted the first comprehensive DNA barcoding study of the Scorpaenidae from Taiwanese waters based on a partial cytochrome c oxidase I (COI) gene of 655 bps. A total of 118 COI sequences were generated from voucher specimens of 66 species (28 genera) identified based on morphological characters. The COI sequences of Parascorpaena maculipinnis, Scorpaena pepo, and Scorpaenopsis orientalis are new to online databases. According to the Kimura-2 Parameter (K2P) genetic distance, the mean interspecific variation (15.61%) was distinctly greater than the mean intraspecific variation (0.22%), suggesting a barcoding gap. The maximum likelihood tree showed that all lineages were supported by high bootstrap values.