Background: Dysbiosis of oral microbiota is the cause of many diseases related to oral and general health. However, few Asia-based studies have evaluated the role of oral microbiota in patients receiving long-term care. Thus, new indications are needed for early prevention and risk management based on information derived from the oral microbiota. Methods: We used next-generation sequencing (NGS) to identify the oral bacterial composition and abundance in patients receiving long-term care: 20 from the outpatient department (OPD) and 20 home-care patients. Their microbial compositions, taxonomy, and alpha/beta diversity were characterized. Results: Microbiota from the two groups showed different diversity and homogeneity, as well as distinct bacterial species. A more diverse and stable microbial population was observed among OPD patients. Our findings indicated that home-care patients had a higher risk of oral diseases due to the existence of dominant species and a less stable microbial community. Conclusion: This work was the first in Taiwan to use NGS to investigate the oral microbiota of long-term care patients. Our study demonstrated the potential use of dominant bacterial species as biomarkers for the risk management of posttreatment complications.