Parrotfish are an important group in the coral reef ecosystem that maintain ecological stability and have a close relationship with coral reefs. Around the world, parrotfish and coral reefs are being destroyed due to human activities and global climate change. Here, we investigated the diversity of parrotfish in the South China Sea (SCS) using DNA barcoding, and initially established a DNA barcode database of the SCS parrotfish. A total of 1620 parrotfish specimens, belonging to 23 species of 6 genera in the family Scaridae, were collected in the SCS, accounting for 64% of the parrotfish species in the SCS. Genetic distance analysis at each taxonomic level showed that the average genetic distance was 0.23% within species, 8.52% within genus and 13.89% within family. The average inter-specific distance was 37.04-fold the intra-specific distance. Barcode gap analysis showed that 6 of the 21 parrotfish species with multiple samples had no barcode gap, resulting in an overall identification success rate of 74%. The ABGD analysis revealed that there could be 37 potential operational taxonomic units (OTUs) and the BIN analysis showed 32 identifiable taxonomic units, which by far exceed the number of morphologically previously known species. Overall, this study complements the lack of parrotfish DNA barcode sequences, and our findings provide an important stepping-stone to further study the diversity of parrotfish in South China. © 2022 by the authors.