In this study, COⅠgene fragments were used as DNA barcodes for the molecular identification in fish larvae and juvenile from Xuwen Jiaowei coral reef sea areas in summer and autumn of 2018—2020, and its applicability to the identification in the early stages of fish was investigated. A total of 199 high quality COⅠsequences of fish larvae and juvenile were obtained, among them, 69 sequences matching to species were identified to the species level, and 110 sequences were identified to the genus, family and order level. In all, 32 taxa of 20 genera in 6 orders and 19 families were successfully identified. Among them, 17 taxa were identified to the species level, 5 taxa to the genus level, 9 taxa to the family level, 1 taxa to the order level, and another 9 taxa were not identified. Gobiidae had the most species and quantity in family level, accounting for 17.07% and 31.16%, respectively, followed by Leiognathidae with 7.31% and 8.04%, respectively. The present study indicated that the proportion of species identification based on DNA barcoding for fish larvae and juvenile in the Xuwen coral reef sea area was relatively low, and the gap of DNA barcode sequences for adult fish species was an important factor. Therefore, it was necessary to develop a reliable DNA barcode database for local adult fish. Combined traditional morphological and molecular method might improve the accuracy in identifying fish larvae and juvenile.