Flavobacterium psychrophilum, the causative agent of bacterial cold-water disease, was first reported in spawning chum salmon Oncorhynchus keta in Hokkaido in 2005. ​In the present study, Hokkaido was divided into five regions by chum salmon stock, and the distribution of this bacteria in spawning chum salmon and the other three species of salmonid fish that return to rivers in each region​—masu salmon O. masou, pink salmon O. gorbuscha, and sockeye salmon O. nerka—was surveyed over a three-year period from 2006 to 2008. ​Samples were collected from the ovarian fluid and kidneys of female salmon, and in some rivers, milt from males was also sampled. ​F. psychrophilum was detected in all rivers surveyed in all regions, and in males and females of all four spawning salmon species. ​The detection rates were high in many rivers (> 70%). ​These results confirm that the pathogen is widespread in Hokkaido regardless of stock, species, or sex of salmons. ​Furthermore, PCR-RFLP genotyping of pathogen isolates from chum salmon revealed multiple genotypes in some rivers. ​In these rivers, the pathogen was thought to have invaded early and differentiated, or to have invaded as multiple strains with different genotypes.