Cheilitis granulomatosa (CG) is a disturbing and persistent idiopathic lip swelling. The cause and treatment has not been wholly elucidated. Some reports infer that CG is mainly associated with dental infection but no firm or reliable microbiological evidence has been provided for a causative organism. This study aimed to evaluate whether microorganisms contribute to the etiology of CG in order to inform appropriate treatment options in clinic. Unstimulated saliva was collected from 15 CG patients who were diagnosed clinically and pathologically and 15 healthy controls (HC). DNA was extracted from the precipitate of the centrifuged saliva for 16s rRNA high-throughput sequencing using the Miseq PE300 platform. The distribution of the microbiome between the two groups was compared. CG patients had a greater microbial flora that was more diverse than the HC. Prevotella, Alloprevotella, Porphyromonas, Actinomyces, Rothia, Fusobacterium, Haemophilus, and Aggregatibacter had a significantly higher abundance in CG patients. In contrast, Streptococcus and Campylobacter were the most abundant genera in HC with a mean relative abundance of 63% and 2%, respectively. The microbiological network indicated that most of the bacteria that were enriched at greater levels in CG patients were likely to be Prevotella, Actinomyces, and Rothia. These have been shown to co-exist with other bacteria. The composition and structure of bacterial communities in CG patients were different from HC. Most of the genera observed in CG patients were associated with periodontitis and pulp infection. These findings might be helpful in understanding the etiology of CG. Further study will be needed to confirm these findings and explore the underlying pathological mechanism.