Background Despite diabetes mellitus and periodontal diseases are mutually exclusive, little is known about particular types of bacteria that may have exacerbated the development of diabetics’ periodontal inflammation. The purpose of this study was to compare the salivary microbiomes of individuals with type 2 diabetes (20–40 years old) who had gingivitis or periodontitis to those who did not. Additionally, we evaluated the relationship between the number of periodontopathogens and the amount of nitrate-reducing bacteria in their salivary microbiome. Methods Saliva was collected, DNA was isolated, the entire 16S ribosomal RNA gene was amplified, and sample libraries were prepared in accordance to the Oxford Nanopore MinION Technology procedure. The relative abundance and bacterial diversity in saliva samples that were pooled according to three groups; T2DM patients without periodontal disease (G1), T2DM patients with gingivitis (G2), and T2DM patients with periodontitis (G3), was measured using bioinformatic methods. Additionally, the relationships between the periodontopathic bacteria ( Porphyromonas gingivalis , Treponema denticola , Tannerella forsythia , and Fusobacterium spp.) and denitrifying community ( Haemophilus , Neisseria , Rothia , and Veillonella ) were assessed. Results The salivary microbiota among people with type 2 diabetes and periodontal disease (gingivitis, G2; periodontitis, G3) showed more bacterial diversity and abundance than that of patients without periodontal disease (G1), according to alpha-diversity analysis (p < 0.0001). The G3 group exhibited the largest abundance of Porphyromonas gingivalis , a periodontopathogen. Additionally, we discovered that periodontopathic bacteria and nitrate-reducing bacteria have different interactions. Moreover, receiver operating characteristic (ROC) analysis demonstrated that, with a high Area Under the Curve (AUC) of 0.93 (p = 0.04), the connection between Fusobacterium spp. and Neisseria was a powerful indicator for distinguishing between gingivitis and periodontitis. Conclusion Results of this study show that the connection between periodontopathic and denitrifying bacteria in the salivary microbiome varies among those with type 2 diabetes mellitus who also have gingivitis or periodontitis. These features may be crucial markers for the early detection and management of gingivitis to avoid periodontitis.