Abstract:[Background] Smoking has become one of the foremost public health problem, which may affect oral health and even host health by changing the salivary microbiome. [Objective] To study the effects of smoking on the salivary microbiome of healthy Chinese people, and to provide enlightenment for the role of smoking in disease-development. [Methods] We collected saliva samples from 167 healthy volunteers, using high-throughput Hiseq sequencing technology for sequencing 16S rRNA gene sequence in the V3?V4 region of samples to research the salivary microbiome of current smokers and never smokers. [Results] The α diversity of the salivary microbiome did not show a significant difference between current smokers and never smokers. However, the relative abundance of the genera Neisseria, Eikenella and Porphyromonas reduced in current smokers, whereas the genera Prevotella, Veillonella, Atopobium, Actinomyces and Megasphaera were significantly increased. Functional analysis from PICRUSt showed that decreased abundance of aerobic metabolism pathways and increased abundance of oxygen-independent carbohydrate metabolism pathways in current smokers. [Conclusion] smoking is a factor influencing salivary microbiome, and then potentially leading to the shifts in functional pathways with implications for smoking-related diseases.