Bacterial diseases are a growing concern in shrimp and fish farming. During the last decade, the global pandemic of acute hepatopancreatic necrosis disease (AHPND) severely impacted the shrimp industry. Vibrio parahaemolyticus carrying the Photorhabdus insect-related (PirAB) toxin was identified as the major causative agent. However, the presence of PirAB toxin over the conjugative plasmid made it easily transmissible across several Vibrio and other bacterial species, making the disease control measures far more difficult. Luminescent vibriosis continues to be a major problem in shrimp hatcheries. Likewise, the increasing number of reports of photobacteriosis and black gill disease (BGD) from shrimp farms calls for the development of suitable rapid diagnostics and remedial measures. Finfish culture is taking momentous shape in the brackishwater and marine sectors. Hence, an appropriate measure to control vibriosis, photobacteriosis, and tenacibaculosis in fish farms is the need of the hour. Bacterial pathogenicity is the interplay between colonization efficiency, production of potent toxins, and the toxin secretion machinery called secretion systems. There is a need to understand these pathogenic factors to differentiate pathogenic from non-pathogenic isolates. In light of growing concerns over antimicrobial resistance (AMR), drug residues, and trade barriers, antibiotic application is highly restricted in aquaculture, especially in the shrimp sector. There is a need to find alternative therapeutic and preventive strategies for controlling bacterial diseases for the sustainable development of aquaculture.