The aquaculture industry has been expanding and more intensification is done to achieve a higher yield. To maintain health, aqua drugs are indiscriminately being used which may create selection pressure on the gut microbiota and ultimately result in the development of antimicrobial resistance (AMR). Researchers across the globe linked the use of antibiotics in aquaculture to the development of AMR. Long-term exposure to the antimicrobials is associated with enhanced resistance in the microbes and changes in the metabolism and composition of gut microbiota. Some examples of commonly used antibiotics in aquaculture are oxytetracycline, ciprofloxacin, enrofloxacin, erythromycin, sulphadiazine, and trimethoprim. The gut microbiome is important in fish development, immunity, and absorption of nutrients. The vast majority of bacterial species (~108 bacteria) inhabit the GIT of fish. However, phylogenetic microbial diversity exists within different fish species. Microbiome diversity is also influenced by the fish’s diet and environmental conditions. Variation also persists in the gut microbiota of freshwater fish and marine fish species. AMR genes from fish can be horizontally transferred to fish-eating birds and other wild animals. Therefore, it is essential to understand microbial diversity and the development of AMR in fish gut microbiota in different ecological niches.