Over 700 bacterial species have been detected in the oral cavity. Several studies have suggested that periodontitis is associated with systemic disorders such as diabetes mellitus, indicating a key role for oral microbiota in human health. However, the relationship between oral microbiota and diabetes has not been well clarified. Therefore, we conducted microbiome analysis of saliva samples obtained from 15 elderly residents (3 with type 2 diabetes mellitus [DM] and 12 without diabetes [non-DM]) at three different nursing homes, as well as 9 young healthy controls (HC). Genomic DNA was extracted from each sample, and then the V4 region of the 16S rRNA gene was amplified and sequenced.Alpha diversity, in terms of operational taxonomic unit richness, was significantly higher in samples from the non-DM group than in those from the HC group. Weighted UniFrac distance analysis showed that salivary microbial communities in the DM group were separately clustered. Furthermore, in the DM group, Actinomyces and Selenomonas showed significantly higher abundance, whereas Alloprevotella showed significantly lower abundance, relative to the non-DM group. Although our findings were limited by the small sample size, oral bacterial diversity in the DM group was clearly different from that in the non-DM group.