Flavobacterium psychrophilum is known as a causative agent of bacterial cold water disease in salmonids and rainbow trout fry syndrome. F. psychrophilum is distributed all over the world, and has been reported to be transmitted horizontally and vertically. This pathogen has never been isolated in Korea until September 2018. Rainbow trout (Body weight= ~ 70 g) were moved from a fish farm to laboratory aquarium, and 34% of fish was killed during the acclimation period. In this study, genome of bacterial isolate F. psychrophilum was sequenced using PacBio RSII platform and was characterized. The genome consists of 2,795,347 bp in a single circular contig, and total 2,737 CDSs were predicted. Phylogenetic relationship was analyzed using 825 of orthologous genes retrieved from 71genomes. Our isolate was most closely related to strains originated from Denmark. This might be due to imported fertilized egg of rainbow trout from Denmark, considering further investigation will be needed. Genome sequencing of major pathogens would provide very important epidemiological information such as origin of location and host species.