On the basis of the 16S rRNA sequence data analysis among the closely related species, the specific primers for Flexibacter maritimus, Flavobacterium branchiophilum, and Cytophaga columnaris were constructed. The specificity in amplifying the 16S rDNA of each species was confirmed by using selected strains of related bacteria and principal fish pathogenic bacteria. A primer pair of MAR 1 and MAR2 could differentiate F. maritimus from other species. The PCR performed with a pair of primers specific to F. branchiophilum failed to amplify the 16S rDNA. However, the PCR with a pair of a specific primer BRA1 and a universal primer 1500R succeeded in specifically amplifying 16S rDNA from F. branchiophilum. The Nucleotide Sequence Database (GenBank) contains two different 16S rRNA sequence data for C. columnaris. On the basis of these data, we produced two primer pairs. A pair of COL1 and 1500R amplified the 16S rDNA from 5 of 7 strains of C. columnaris, and a pair of COLa and COLb worked for the rest of the strains. In addition, these two groups within C. columnaris were supported by PCR-RFLP.