Abstract: Objective：To investigate the composition and characteristics of oropharyngeal and pulmonary bacterial microbiota of infants with pneumonia less than 6 months old. Methods：Patients who were diagnosed as pneumonia and aged less than 6 months old were recruited from the respiratory ward of Children's Hospital of Fudan University. The oropharyngeal swabs and bronchoalveolar lavage fluid (BALF) was collected to extract DNA. The V3V4 region of the bacteria's 16S rDNA gene was amplified by PCR. Sequencing of the purified amplicons was performed and analyzed. Results：Overall, 24 infants with pneumonia were recruited and further analyzed. The top 5 abundant bacteria in the oropharyngeal were Streptococcus, Pseudomonas, Prevotella_7, Veillonella and EscherichiaShigella. The top 5 abundant bacteria in the lung were Pseudomonas, Streptococcus, Prevotela_7, Klebsiella and Rothia. The pulmonary microbiota had much more particular bacteria. The oropharyngeal microbiota richness was significantly lower in the 24 patients as compared with the microbiota of the pulmonary (P＜0.05). The diversity was significantly lower in pulmonary microbiota (P＜0.05). At the genus level, the oropharyngeal microbiota was dominated by Streptococcus (53.55%) and Pseudomonas (13.39%); the pulmonary microbiota was also dominated by Pseudomonas (73.06%) and Streptococcus (16.91%). The relative abundance of streptococcus and pseudomonas was significantly different between the oropharyngeal and pulmonary microbiota (P＜0.05). Conclusion：There are significant changes in the oropharyngeal and pulmonary microbiota of infant with pneumonia. The composition of oropharyngeal and pulmonary microbiota is similar and the proportion of each bacteria is different.