Coral reef ecosystems harbors high biodiversity, which makes them among the most biologically complex and valuable ecosystems on the planet. Coral reef fish represents a crucial functional group within these ecosystems. However, the species diversity of coral reef fish in the South China Sea remains largely underestimated. During an investigation of coral reef fish samples from the South China Sea, we identified a new record of coral reef fish in China through morphological comparison and molecular identification. We employed a comparative analysis of 18 morphological characteristics alongside molecular identification with COI as the molecular maker. MitoZ was used to assemble the complete mitochondrial genome of the record after whole genome resequencing. After extraction of the COI gene, a maximum likelihood phylogenetic tree was constructed in RAxML, and a Bayesian inference tree was constructed in Beast2. Genetic distances were estimated via the Kimura 2-parameter (K2P) model implemented in MEGA 11. Thirteen coding genes were extracted and concatenated to construct the maximum likelihood phylogenetic tree in PhyloSuite. We identified the species as a new record of coral reef fish in China, which was Pomacentrus cheraphilus (collected from Sanya City, Hainan Province). The morphological characteristics of the newly collected specimens were described and measured (Table 1 and Fig. 1), and their phylogenetic relationships were analyzed (Figs. 2﹣4 and Appendices 1 and 2). The discovery of the new record of coral reef fish in China enriches the diversity of China’s marine fish fauna and indicates that further enhancement of surveys and conservation efforts is required for the biodiversity of coral reef ecosystems in the South China Sea.