Antibiotics are widely used in mariculture industry, and this study attempts to determine the extent of water and sediment pollution by antibiotic residues in 13 major mariculture sites in China. Through chemical and molecular biology analysis, the results showed that the total concentrations of sulfonamides and tetracyclines were in the range 62.0–373.8ngL−1 and 0.2–259.1ngL−1 respectively in water samples, and in the range 0.19–1.59ngg−1 dry weight and 3.45–74.84ngg−1 dry weight respectively, in sediments samples. The occurrence of antibiotic resistance genes (ARGs) was detected in all sites. Compared with the tetracyclines resistance genes, the absolute copy number and relative abundance of the sulfonamides resistance genes were 4.3 times and 2.3 times higher in water and sediment from the mariculture sites, with the dominant resistance genes being sul2. The abundance of sul3 in the water phase was significantly correlated with the concentrations of sulfamerazine, while the abundance of sul2 in the sediment phase was significantly with sulfadiazine concentrations. The abundance of tetM in the sediment phase was significantly correlated with the concentrations of oxytetracycline. The findings demonstrate the persistence of antibiotic residues and ARGs in major mariculture sites in Southeast China. Total concentrations of the target antibiotics in water and sediments from mariculture sites in SE China. Display omitted •11 antibiotics were detected in water and sediments from mariculture sites in China.•Water samples were dominated by sulfadiazine.•Sediment samples were dominated by doxycyclinehyclate.•Antibiotic resistance genes were dominated by sul2 in both water and sediments.•Linear relationships between log Koc and log Kow, and between log Koc and log MW.