Abstract: In order to reveal the occurrence characteristics of antibiotic resistance genes (ARGs) in culture environment of eel, through the collection of the culture environment samples for eel (sediment and aquaculture water), the species and abundance of ARGs in the culture environment of eel were studied by using the analysis methods of high-throughput sequencing technology and functional metagenomics. The results showed that there were significant differences in the structure composition of dominant microflora between the aquaculture sediment and aquaculture water of eel. The dominant microflora genera of sediment included Proteobacteria, Chloroflexi, Actinobacteria, Cyanobacteria, Gemmatimonadetes and Bacteroidetes, while the dominant microflora genera of aquaculture water included Proteobacteria, Bacteroidetes and Verrucomicrobia. Compared with the resistance gene database, there were 38 ARGs in 10 categories in the sediment, and 29 ARGs in 9 categories in the aquaculture water, among which the resistant types with high abundance were tetracyclines, sulfonamides and bacitracin antibiotics. Therefore, the results of this study could provide reference for the rational use of antibiotics during the eel culture, and also show the feasibility and superiority of metagenome sequencing technology in the detection of ARGs in the environment.