One major source of antibiotic contamination in the sea is from aquaculture. We monitored concentration of commonly used antibiotic classes and antibiotic resistance genes (ARGs: tet(M), sul1, sul2 and sul3) in seven main aquaculture production stations in Peninsular Malaysia and detected twenty-three antibiotics. Tetracyclines, sulfonamides and quinolones were the most frequently detected antibiotic classes, 2 indicating a wide distribution of antibiotics in Malaysian aquaculture farms.Oxytetracycline, tetracycline and minocycline were the common tetracyclines (LOQ-2.45× 10 2 ng/L) detected, while sulfamerazine and sulfathiazole were commonly detected sulfonamides (LOQ-2.82× 2 ng/L) among the farms. For quinolones (LOQ-9.58 × 10 5 ng/L), enrofloxacin, nalidixic acid, and ofloxacin were the most 31 common. Relative to Asian aquaculture farms, the residues detected here were at low 32 or moderate levels except for quinolones. The dendrogram and heatmap revealed 33 three groups of antibiotic concentration patterns but with no differences in the types of antibiotics usage among aquaculture farms were observed. The ARGs (10 -3 copies/16S) were detected in more than 90% of the sites except for sul3. There was also high ecological risks of ciprofloxacin, enrofloxacin, norfloxacin and lincomycin for cyanobacteria and algae in Kelantan, Perak and Pahang. This is the first study to shed light on the antibiotic contamination, ARGs in aquaculture systems and its potential ecological risk in the coasts of Malaysia. This study will be useful to develop effective management of aquaculture wastewater in order to mitigate antibiotic pollution and transmission of ARGs to humans through the food chain.