Background: Studies have reported a high prevalence of periodontal disease in individuals with intellectual disability (ID). The aim of this study was to compare the relative abundance of periodontal pathogens (red, orange, yellow, purple, and green complexes) between individuals with ID and healthy controls.Methods: Of the 31 subjects enrolled in this study, 16 with severe ID were selected from the outpatient clinic of the Special Care Dentistry of Hiroshima University Hospital, and 14 healthy subjects were selected from the outpatient clinic of another department at the same hospital. Dental plaque was sampled after oral examination. Decayed, missing, and filled permanent teeth (DMFT) counts were obtained and periodontal measurements were taken using the papillary-marginal-attached (PMA) index, plaque index (PI), gingival index (GI), and probing depth (PD). Gene sequencing (16S rRNA) was performed for each sample using next-generation high-throughput sequencing methods. The relative abundance of the periodontal pathogens and the clinical parameters were compared. An unpaired t-test was used to compare the oral health status in both groups and analysis of covariance was performed to compare the relative abundance of each pathogen.Results: No statistically significant difference in DMFT was observed between the two groups. However, significant differences in the median PMA index, PI, and GI were noted between the groups (P < 0.0001). In addition, the mean PD in the ID group was significantly higher than that in the control group (P < 0.0001). The relative abundances of Tannerella spp. and Treponema spp. were significantly higher in the ID group when compared to the control group at the genus level (P = 0.0383 and 0.0432, respectively); alternatively, the relative abundance of Porphyromonas spp. was significantly lower in the ID group (P < 0.0001).Conclusions: The PMA index, PI, GI, and PD were significantly lower in the ID group than in the control group. On the other hand, no significant difference in DMFT was observed between the two groups. Furthermore, our findings indicate that Tannerella forsythia might be more closely associated with periodontal disease than Porphyromonas gingivalis in individuals with ID.