Abstract Population genetic analysis of Flavobacterium psychrophilum using multilocus sequence typing (MLST) data has identified a genetic lineage consisting of sequence types (STs) associated with epidemic spread and high mortality in farmed rainbow trout (Oncorhynchus mykiss). To identify phenotypic characteristics that discriminate epidemic F. psychrophilum STs from sporadically occurring STs, a set of traits of isolates/STs (n = 32) with distinct genetic background and clinical impact was studied in vitro. The results showed that epidemic and sporadic STs could not be discriminated by their resistance to povidone-iodine or iron starvation or by their ability to hydrolyze elastin and gelatin. Antimicrobial resistance against flumequine, oxolinic acid and oxytetracycline was significantly more prevalent (p