The control of food poisoning associated with fish and fish products is challenging, even in the developed world. Injured cells of bacterial pathogens, generated by various stressors during food processing, are considered to be an important risk factor in food poisoning incidents. It is important to accumulate more knowledge on the physiology, genetics, and molecular biology of injured bacterial cells related to fish and fish products, and also to apply this knowledge to the development of new technologies. Here, we introduce recent advances in the physiology and genetics of Vibrio parahaemolyticus and Listeria monocytogenes and discuss future directions of the risk control of pathogens in fisheries.