Objective To analyze the difference of salivary microbiome between the patients with functional dyspepsia and healthy controls.Methods Saliva samples were collected from the patients with functional dyspepsia and healthy control.Genomic DNA of the samples was extracted,and the high-throughput sequencing technology was used to conduct DNA sequence of 16S rRNA-V4 region.Subsequently,all the data were performed by the bioinformatic analysis.Results The salivary microbiome in the functional dyspepsia group was dominated by Proteobacteria,while Bacteroidetes was the top microbiota in the heathy control group.In the functional dyspepsia group,the Chao1 index,ACE index,Shannon index and Simpson index were 1 295,1 351,4.93 and 0.90 respectively.In the healthy control group,the above indexes were 1 001,1 351,5.28 and 0.92 respectively.The PCoA ba sically separated the microbiome composition of the two groups.Sixteen kinds of microbiota were significantly different between two groups using linear discriminant analysis effect size tool,including Bacteroidetes,Prevotella,Prevotellaceae,Neisseria,Betaproteobacteria and Proteobacteria,etc.Conclusion Saliva in the patients with functional dyspesia has characteristic microbiome composition,which is dominated by Proteobacteria,but the richness and diversity between the two groups have no difference.Neisseria is one of the significantly different bacteria between the two groups.