Wild fisheries are declining due to over-fishing, climate change, pollution and marine habitat destructions among other factors, and, concomitantly, aquaculture is increasing significantly around the world. Fish infections caused by pathogenic bacteria are quite common in aquaculture, although their seriousness depends on the season. Drug-supplemented feeds are often used to keep farmed fish free from the diseases caused by such bacteria. However, given that bacteria can survive well in aquatic environments independently of their hosts, bacterial diseases have become major impediments to aquaculture development. On the other hand, the indiscriminate uses of antimicrobial agents has led to resistant strains and the need to switch to other antibiotics, although it seems that an integrated approach that considers not only the pathogen but also the host and the environment will be the most effective method in the long-term to improve aquatic animal health. This review covers the mechanisms of bacterial pathogenicity and details the foundations underlying the interactions occurring between pathogenic bacteria and the fish host in the aquatic environment, as well as the factors that influence virulence. Understanding and linking the different phenomena that occur from adhesion to colonization of the host will offer novel and useful means to help design suitable therapeutic strategies for disease prevention and treatment.