OBJECTIVE This study investigateed the influence of complete denture on oral bacteria flora. METHODS Bateria plaque samples in oral mucosa, saliva and denture surfaces in 11 edentulous patients were collected, then the 16S rRNA gene clone libraries were constructed. Pyrosequencing was used to analyze the 16S rRNA gene V3~V4 regions, oral bacteria flora were classified and identified. RESULTS There were 64800 sequences in complete denture-wearing subjects, Streptococcus mitis, Gemella haemolysans, Rothia mucilaginosa, Porphyromonas sp, Neisseria zoodegmatis, Granulicatella elegans, Acinetobacter baumannii, Pseudomonas citrinum, Granulicatella adiacens and Fusobacterium canifelinum were the predominant species (37416 sequences). The species of denture tissue surface were similar to these of buccal vestibule after wearing denture, and the species of denture smooth surface were similar to these of tongue ventrum and the floor of mouth. CONCLUSIONS The effect of complete denture on oral flora is still limited, and the composition of oral flora is influenced by many other factors.