The aim of this study was to evaluate molecular and phenotypic methods for the identification of nonhemolytic streptococci. A collection of 148 strains consisting of 115 clinical isolates from cases of infective endocarditis, septicemia, and meningitis and 33 reference strains, including type strains of all relevant Streptococcus species, were examined. Identification was performed by phylogenetic analysis of nucleotide sequences of four housekeeping genes, ddl, gdh, rpoB, and sodA; by PCR analysis of the glucosyltransferase (gtf) gene; and by conventional phenotypic characterization and identification using two commercial kits, Rapid ID 32 STREP and STREPTOGRAM and the associated databases. A phylogenetic tree based on concatenated sequences of the four housekeeping genes allowed unequivocal differentiation of recognized species and was used as the reference. Analysis of single gene sequences revealed deviation clustering in eight strains (5.4%) due to homologous recombination with other species. This was particularly evident in S. sanguinis and in members of the anginosus group of streptococci. The rate of correct identification of the strains by both commercial identification kits was below 50% but varied significantly between species. The most significant problems were observed with S. mitis and S. oralis and 11 Streptococcus species described since 1991. Our data indicate that identification based on multilocus sequence analysis is optimal. As a more practical alternative we recommend identification based on sodA sequences with reference to a comprehensive set of sequences that is available for downloading from our server. An analysis of the species distribution of 107 nonhemolytic streptococci from bacteremic patients showed a predominance of S. oralis and S. anginosus with various underlying infections.The genus Streptococcus currently consists of more than 50 species, most of which belong to one of six phylogenetic clusters that are revealed by comparative analysis of 16S rRNA gene sequences. In addition to the pyogenic group, which includes the traditional pathogenic species (i.e., hemolytic streptococci), these clusters are the anginosus group, the mitis group, the salivarius group, the bovis group, and the mutans group (30,34). Many of the species of these five clusters are major constituents of the commensal microbiota of the human oral cavity and upper respiratory tract and are occasionally implicated in various pathologies. The anginosus group, formerly called "Streptococcus milleri" in some parts of the world (16), includes three recognized species (Streptococcus anginosus, Streptococcus intermedius, and Streptococcus constellatus) that are primarily associated with suppurative infections of tissues of the mouth and various body sites, including the meninges (9,37,44,54,56). The mitis group currently includes