Streptococcus parauberis is a pathogen of streptococcosis in turbot Scophthalmus maximus and the Japanese flounder Paralichthys olivaceus. S. parauberis isolates from diseased Japanese flounder have been classified into several serological phenotypes. In this study we analyzed the DNA sequence of the genetic locus for capsular polysaccharide (CPS) biosynthesis of S. parauberis KRS02083 (subserotype Ia), NUF1003 (subserotype Ib), NUF1071 (subserotype Ic), NUF1032 (serotype II), 2007-1 (nontypeable/PFGE cluster I) and NUF1095 (nontypeable/PFGE cluster III) to elucidate the genetic basis for serological diversity. As a result, three kinds of cps locus were revealed among serotypes and subserotypes, namely the loci for subserotype Ia, subserotypes Ib/Ic and serotype II. The genetic structure of cps loci suggests that the capsules of S. parauberis are synthesized through the Wzy-dependent pathway. Subserotypes Ib and Ic possessed the same genetic structure, although single-base substitution at several regions or insertion of an IS (insertion sequence) element was found in subserotype Ic. The nontypeable strains, which agglutinated with both serotypes I and II antisera, possessed the same genetic structure as subserotype Ib/Ic or serotype II with single-base substitution at several regions.