Abstract: Feeding analysis of fish at early growth stages is helpful to understand its food source and functional role. Comprehensively and accurately obtaining the information of food species is critical for this endeavor. The development of high-throughput sequencing (HTS) technology has brought unprecedented opportunities and challenges to dietary analysis of animals. Molecular techniques have been widely used for analyzing diet composition of different animals, among which HTS has been successfully used on marine fish. But the accuracy and suitability of HTS have not been confirmed and compared with traditional Sanger sequencing on the dietary analysis of juvenile fish yet. In this study, a comprehensive comparison was performed between traditional Sanger sequencing and HTS on the diet analysis of Scatophagus argus juveniles, an important commercial fish in South and Southeast Asia. The juvenile fish were collected near a wharf in Daya Bay, China, and analyzed both by traditional Sanger sequencing and HTS methods targeting 18S rDNA gene. Results showed that the diet composition was complicated and dominated by ciliates and bryozoans, indicating an omnivorous feeding of juveniles. Sixty-seven effective sequences were obtained and 21 food species were identified by Sanger sequencing, while 35 food species from 17000 effective sequencings were identified by HTS. The food groups obtained by both techniques were similar. HTS had advantages in dietary coverage due to the large amount of data. HTS detected preys of dinoflagellates and brown algae which were not found in Sanger sequencing. In addition, HTS could provide semi-quantitative information to some extent based on a large amount of data, overcoming the deficiency of Sanger sequencing in quantitative research. Our results suggested that HTS is much more powerful than Sanger sequencing on diet analysis of juvenile fish, which can provide more details and comprehensive information about the feeding of juvenile fish.