Nonhemolytic streptococci (NHS) cause serious infections, such as endocarditis and septicemia. Many conventional phenotypic methods are insufficient for the identification of bacteria in this group to the species level. Genetic analysis has revealed that single-gene analysis is insufficient for the identification of all species in this group of bacteria. The aim of the present study was to establish a method based on sequence analysis of the 16S-23S intergenic spacer (ITS) region and the partial gdh gene to identify clinical relevant NHS to the species level. Sequence analysis of the ITS region was performed with 57 NHS reference or clinical strains. Satisfactory identification to the species level was achieved for 14/19 NHS species included in this study on the basis of sequence analysis of the ITS region. Streptococcus salivarius and Streptococcus vestibularis obtained the expected taxon as the best taxon match, but there was a short maximum score distance to the next best match (distance, <10). Streptococcus mitis, Streptococcus oralis, and Streptococcus pneumoniae could not be unambiguously discriminated by sequence analysis of the ITS region, as was also proven by phylogenetic analysis. These five species could be identified to the group level only by ITS sequence analysis. Partial gdh sequence analysis was applied to the 11 S. oralis strains, the 11 S. mitis strains, and the 17 S. pneumoniae strains. All except one strain achieved a satisfactory identification to the species level. A phylogenetic algorithm based on the analysis of partial gdh gene sequences revealed three distinct clusters. We suggest that sequence analysis of the combination of the ITS region and the partial gdh gene can be used in the reference laboratory for the species-level identification of NHS.Streptococci are a heterogeneous group of bacteria consisting of more than 50 species. In addition to the traditional pathogenic pneumococci and hemolytic streptococci (HS), many species of non-HS (NHS), which are part of the commensal microbiota in the human body, are known to be opportunistic pathogens that cause serious systemic and local infections. These infections include subacute infective endocarditis (24), bacteremia in immunocompromised patients (19, 44), brain abscesses (34), meningitis (35), and pneumonia (5).There are reports describing associations between some specific species and clinical manifestations. Streptococcus gallolyticus and Streptococcus lutetiensis in the bovis group are reported to have a strong association with colon cancer (31-33). Streptococcus anginosus and Streptococcus intermedius in the anginosus group are associated with abscess formation (9, 26), and Streptococcus mitis and other normal oral commensals have a strong association with infective endocarditis (6, 10, 22). The precise species-level identification of NHS from relevant clinical specimens is crucial to making the right diagnosis and understanding the pathogenesis of the infection.The conventional phenotypic tests do not always allow accurate ident...