The emergence of antimicrobial resistance is one of the major challenges addressed by the aquaculture industry in recent years. Bacterial resistance to antibiotics is mainly due to the rampant prophylactic use of antibiotics in fish farms. The persistent nature of antibiotics in the system ultimately leads to the development of resistance in environmental bacteria; consequently, resistance can be transmitted to pathogenic and human commensal bacteria via horizontal gene transfer. Increased attention has been paid to antibiotic resistance in aquatic environments due to its significant threat to human health. High-throughput genomic technologies can be used for metagenomic surveillance of antibiotic resistance determinants in environmental bacteria.Continuous monitoring programmes and timely detection of resistant pathogens are unavoidable to curb antimicrobial resistance dissemination in the aquaculture system. The present review focuses on different sources of antimicrobial resistance in aquaculture systems, the current status of antimicrobial use, antimicrobial resistance in ornamental and food fish of freshwater systems, molecular mechanisms involved in resistance development, antibiotic residue in the aquaculture environment and metagenomics-based detection of antimicrobial resistance in the aquaculture environment.