Aquaculture is an important food source worldwide but one of its main problems is the spread of infectious diseases caused by Gram-negative pathogenic bacteria that results in considerable economic losses. Since siderophores, low molecular weight organic compounds involved in the iron-uptake mechanisms of the bacteria, are critical for the growth and virulence of the producer pathogens, the bacterial iron acquisition systems are promising targets for the design of new antimicrobial strategies. In this chapter, the current chemical knowledge of the siderophores involved in the iron-uptake mechanisms of Gram-negative pathogenic bacteria Vibrio anguillarum, Photobacterium damselae subsp. piscicida, and Aeromonas salmonicida subsp. salmonicida, responsible for the main fish infectious diseases Vibriosis, photobacteriosis, and furunculosis, respectively, is summarized. The isolation, structural elucidation, and the chemical synthesis of the siderophores biosynthesized from those bacteria are displayed. Their involvement in the iron-uptake mechanisms, virulence importance, and the application in the development of new strategies to fight against the infectious diseases will be also discussed.