Investigating the composition and functional analysis of the intestinal microbiome of wild leptocephalus larvae has significant scientific and practical value for predicting their nutritional needs and developing appropriate initial diet. The study identified the species of leptocephalus larvae captured during the 2022 and 2023 scientific expeditions of the "Songhang" research vessel in Western and Central Pacific Ocean using DNA barcoding technology. Additionally, 16S rDNA high-throughput sequencing was employed to sequence the intestinal samples of the leptocephalus larvae, aiming to analyze the intestinal microbial community structure and identify dominant microflora and their related functions. Results showed that 14 of 16 captured leptocephalus larvae were identified to the species level, including Ariosoma majus, Thalassenchelys coheni, Ariosoma megalops, Gnathophis longicauda, Ariosoma meeki, Muraenidae sp. KY17-483, and Gymnothorax zonipectis. The other two leptocephalus larvae were identified to the genus level, Gymnothorax and Gnathophis. Sequencing revealed that the dominant bacterial groups in the intestinal microbiota of pacific leptocephalus larvae were Proteobacteria, Bacteroidetes and Firmicutes. At the genus classification level, Psychrobacter and Acinetobacter exhibited relatively high abundance. However, there were some differences in the intestinal microbiota between different species and sampling sites. Furthermore, functional prediction analysis showed that intestinal microbiota involved in metabolism had the highest relative abundance, and functional pathways related to ‘amino acid transport and metabolism' were the most enriched. These data suggested that leptocephalus larvae have a higher demand for protein. Our results preliminarily elucidated the diverse composition of the intestinal microbiota in leptocephalus larvae, providing a reference for studying their feeding habits and the development of starter feeds during the artificial breeding of Japanese eels.