Abstract: This research focus on identification of fish eggs and larvae collected in Xiamen waters. The samples were distinguished to 2 types of fish eggs and 3 types of fish larvae by morphological characters and were identified as 3 species fish eggs and 4 species fish larvae by DNA barcoding technology. In which, there were six species and one genus were identified, including Thryssa kammalensis egg, Nuchequula nuchalis egg, Tridentiger trigonocephalus larva, Tridentiger barbatus larva, Konosirus punctatus larva, Platycephalus indicus larva and Ambassis sp. egg. The results showed that molecular technology was necessary in identification of fish eggs and larvae to species, especially those species without enough morphological characters. By using automation and standardization system, DNA barcoding technology can identify the species of fish eggs and larvae effectively. This technology with the advantages of high reliability, excellent repetition and less error is a powerful complement for traditional identification by morphology and has wide application prospects in the study of ichthyoplankton diversity.