Many opportunistic pathogens can alternate between inside- and outside-host environments during their life cycle. The opportunistic fish pathogen Flavobacterium columnare is an inhabitant of the natural microbial community, and causes significant yearly losses in aquaculture worldwide. The bacterium grows in varying colony morphotypes that are associated with either virulence (rhizoid type), or resistance to starvation and phages (rough type). Rough type strains can arise spontaneously or be induced by phage infection. To identify the determinants of morphotype fitness, we measured virulence, growth parameters, biofilm forming ability and resistance to amoeba and ciliate predation of both morphotypes in thirteen F. columnare strains. The (phage-sensitive) rhizoid type had a fitness advantage over the rough type in virulence, growth rate and maximum population size. Phage-induced rough type was found to be significantly weakest in resisting both ciliate and amoeba predation, and produced more biofilm in the presence of amoebae, whereas the spontaneous rough types did not differ from rhizoid in biofilm production. In co-culture experiment, the ciliate population sizes were higher when co-cultured with rough type than with rhizoid type. Our results thus suggest that the resistance to phages and starvation of the F. columnare rough type may have strong a trade-offs, as the performance of the ancestral rhizoid type is better under environmental conditions. This article is protected by copyright. All rights reserved.