Streptococcus anginosusis a commensal Streptococcal species that is often associated with invasive bacterial infections. However, little is known about its molecular genetic background. Many Streptococcal species, includingS. anginosus, harbor clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems. A CRISPR-Cas type II-A system as well as a type II-C system have been reported for this species. To characterize the CRISPR-Cas type II systems ofS. anginosusin more detail, we conducted a phylogenetic analysis of Cas9 sequences from CRISPR-Cas type II systems with a special focus on streptococci andS. anginosus. In addition, a phylogenetic analysis ofS. anginosusstrains based on housekeeping genes included in MLST analysis, was performed. All analyzed Cas9 sequences ofS. anginosusclustered with the Cas9 sequences of CRISPR type II-A systems, including the Cas9 sequences ofS. anginosusstrains reported to harbor a type II-C system. The Cas9 genes of the CRISPR-Cas type II-C systems of other bacterial species separated into a different cluster. Moreover, analyzing the CRISPR loci found inS. anginosus, two distinctcsn2genes could be detected, a short form showing high similarity to the canonical form of thecsn2gene present inS. pyogenes. The second CRISPR type II locus ofS. anginosuscontained a longer variant ofcsn2with close similarities to acsn2gene that has previously been described inStreptococcus thermophilus.Since CRISPR-Cas type II-C systems do not contain acsn2gene, theS. anginosusstrains reported to have a CRISPR-Cas type II-C system appear to carry a variation of CRISPR-Cas type II-A harboring a long variant ofcsn2.