Objective Traditional identification of fish eggs and larvae mainly relies on morphological characteristics, which can generally only reach the family or genus level and cannot achieve accurate species discrimination. As a rapid and stable molecular tool unaffected by developmental stages, deoxyribo nucleic acid (DNA) barcoding has been widely applied to the identification of early fish resources. However, a comprehensive local DNA barcode database is still lacking for the coastal waters of southern Fujian, and public databases suffer from incomplete sequence coverage and non-standard annotation, which reduce the accuracy of species identification. This study aims to explore the applicability of DNA barcoding in identifying fish eggs and larvae in the coastal waters of southern Fujian, clarify their species composition and variations, and provide a scientific basis for the conservation of fishery resources in this area.

Methods Based on the mitochondrial COⅠ gene, we performed amplification, sequencing and molecular identification of fish eggs and larvae from the coastal waters of southern Fujian, calculated K2P genetic distances, constructed phylogenetic trees, and analyzed variations in community structure.

Results The results showed that a total of 103 valid sequences were obtained, of which 82.5% were identified to the species level and the remaining sequences were all identified to the genus level. The intra-specific, inter-specific within genus, and inter-generic K2P genetic distances were 0.003, 0.101 and 0.185, respectively, showing an obvious barcode gap. The topology of the phylogenetic tree was basically consistent with the existing evolutionary framework of fishes. Restricted by the lack of local population sequences and insufficient coverage of non-commercial fish species in public databases, 18 sequences could only be identified to the genus level. In total, 23 fish eggs and larvae belonging to 18 genera, 14 families and 6 orders were identified. Perciformes was the absolutely dominant order, and the dominant families included Sciaenidae, Scorpaenidae, Leiognathidae and Engraulidae. Influenced by overfishing, reclamation and habitat degradation, the community was dominated by small low-value fish such as Stolephorus commersonnii, Omobranchus ferox and Photopectoralis bindus. The species composition changed significantly compared with historical surveys, which was consistent with the trend of miniaturization and low-valued tendency of fishery resources in the coastal waters of southern Fujian.

Conclusion This study verifies that DNA barcoding is suitable for the species identification of fish eggs and larvae in the coastal waters of southern Fujian. The community structure of early fish resources has changed obviously due to human activities and environmental disturbance. Establishing a local DNA barcode database, adopting combined identification with multi-gene markers and morphological methods, and improving the monitoring system of early fish resources will provide reliable support for fishery resource conservation and ecological restoration.