As the most frequent infectious disease among children worldwide, dental caries have a strong relationship with oral hygiene status, specifically in the development of infection. However, the study regarding the identification and distribution of oral are limited. The oral community may affected by the differences in geographical location, age, diet, lifestyle, socio-economic status and oral hygiene status. Here, we studied the oral hygiene status by examining the composition and proportion of oral species in saliva of Japanese children. Microbial samples collected from 15 Japanese children divided into three oral hygiene groups were cultured under anaerobic conditions after homogenization and dilution, and inoculated onto brain heart infusion and selective medium agar. Genomic DNA was extracted from each isolate. species were detected by one-step PCR using species-specific primers. To analyse the phylogenetic properties of the unknown strains, PCR amplification and sequence analysis of were conducted for 10 representative strains. Although was found as the predominant species among all groups, its prevalence was significantly lower in the children with poor oral hygiene than in those with good oral hygiene. was the prevalent species in the poor oral hygiene group. Approximately 10% of the isolated strains were not classified to any established species; the phylogenetic analysis showed that they were most closely related to This study demonstrates that the composition and proportion of oral species in the saliva of Japanese children is correlated with different oral hygiene status. Changes in detection ratios of and can be useful indicators of oral hygiene status. Furthermore, new strains closely related to were isolated from the saliva of Japanese children.