Aeromonas are often found in aquatic environments, in which they may cause disease in marine fish and are associated with seafood-related outbreaks worldwide. The objective of this study was to determine the antibiotic resistance and polymyxin B resistance mechanism of 200 isolates of Aeromonas spp. obtained from apparently healthy yellow catfish, hybrid snakehead and associated water, respectively, in seven intensive aquatic farms in Guangdong, China. Six Aeromonas species were identified, of which A. veronii was the most prevailing species. The susceptibility to 16 antimicrobial agents was evaluated by the broth microdilution method. All isolates were resistant to at least one antibiotic, with the highest resistance percentage to ampicillin (99.0%), and relative lower resistance rates to tetracycline (49.0%) and trimethoprim-sulfamethoxazole (43.0%). More than half of the strains were multi-drug resistant (MDR). Seven strains were resistant to polymyxin B with minimum inhibitory concentration (MIC) values of 4–512 mg/L, which were mediated by novel variable mcr-3-like and mcr-7-like genes. The results of this study indicated that yellow catfish, hybrid snakeheads and associated environments in intensive fish farms are reservoir of antibiotic resistant Aeromonas which may contaminate associated fish products and spread through food chain to human, representing a potential public health risk.