Although S. suis attracts public attention as a major swine and human pathogen, this bacterium is sometimes isolated from other animals. In the diagnostic service of NIAH-NARO, we have encountered isolates from ruminants, which were identified as S. suis by commonly used methods for the identification of S. suis. However, in the isolates, S. suis-like bacteria were actually included, and this caused confusion in veterinary diagnostic laboratories. For accurate diagnosis of streptococcal diseases in ruminants, we re-identified 64 “S. suis” isolates from ruminants and their environments by S. suis-specific recN-PCR and 16S rRNA gene sequencing. We found that only 10.9% of them were authentic S. suis and that 94.6% of the isolates from the lesions of diseased animals were closely related to S. suis serotype 33 reference strain, which has recently been proposed as a novel species Streptococcus ruminantium (Tohya et al., in press). Because prevalence of S. suis and S. ruminantium in the tonsils of healthy cattle was comparable (29.7% and 18.8%, respectively) in our investigation in a meat inspection center, frequent S. ruminantium isolation from diseased ruminants implies that S. ruminantium more preferentially causes diseases in ruminants than S. suis. Unlike S. suis, potentially virulent clonal groups were not found by PFGE analysis. Draft genome sequence analysis of representative S. ruminantium isolates revealed the diversity of the cps gene clusters. In this study, we also developed a S. ruminantium-specific PCR. These tool and information will contribute to a deeper understanding and accurate diagnosis of streptococcal infections in ruminants.