Flavobacterium psychrophilum and Vibrio anguillarum are important fish pathogens in salmonid aquaculture worldwide. Due to increased antibiotic resistance, pathogen control using bacteriophages has been explored as a possible alternative treatment. However, the effective use of bacteriophages in pathogen control requires overcoming the selection for phage-resistance in the bacterial populations. We have examined several anti-phage defense mechanisms in these fish pathogen: 1) Mutation-based resistance mechanisms using whole-genome sequencing of the ancestral phage-sensitive strain and phage-resistant isolates, 2) Quorum sensing regulated regulation of phage receptor expression and 3) Masking of phage receptors by aggregation/biofilm formation. Genomic analysis of mutational changes in phage resistant strains demonstrated mutations in genes related to cell surface properties, gliding motility, and biosynthesis of lipopolysaccharides. The genetic changes were supported by direct measurements of changes in bacteriophage adsorption rates, biofilm formation properties and secretion of extracellular enzymes, suggesting that resistance mutations were associated with a number of derived effects on the physiological properties of the pathogen, including reduced virulence. Our results also demonstrated that some fish pathogens employ non-mutational strategies to prevent phage infection: Quorum sensing regulation is used to choose between the two complementary anti-phage defense strategies involving either downregulation of receptor expression or cell aggregation. The prevalence of non-mutational defense mechanisms in some strains suggests a co-existent lifestyle rather than the classical phage-bacterial co-evolutionary arms race. Overall, phage-driven physiological and behavioral changes associated with phage defense potentially have large implications for the impact of the pathogen in aquaculture, and these effects of phage resistance on host properties are therefore important for the ongoing exploration of phage-based control of fish pathogens.