Yersinia (Y.) ruckeri has been recognized as a serious bacterial pathogen to several kinds of fish, including rainbow trout. However, there are no reports about the characteristics and pathogenicity of Y. ruckeri isolated from farm-cultured eels. In this study, we isolated and characterized Y. ruckeri from the farm-cultured eel Anguilla japonica in Korea. We investigated the phenotypic and genotypic characteristics of Y. ruckeri and tested the virulence of Y. ruckeri isolates on experimentally infected eels. Examination of the flagellar morphology of Y. ruckeri by electron microscopy showed peritrichous flagella in its cell body. Biochemical reaction studies showed overall identical profiles between the isolates and the reference strain of Y. ruckeri in API 20E and API ZYM tests. We sequenced the 16S rRNA of the Y. ruckeri (1,505 bp) for the genotypic characterization (National Center for Biotechnology Information accession number EU401667). Comparison of the 16S rRNA sequences with previously reported Y. ruckeri strains revealed similar phylogenetic relationships. In the virulence assay of the Y. ruckeri on eels, the eels exhibited listlessness, but Y. ruckeri was reisolated from those of the gills and kidneys.