[Objective] Traditional fermented camel milk is a valuable source of food for people living in the arid areas, and it is often used to treat a variety of disease with good effects. Its nutritional and medical functions are closely related to its abundant lactic acid bacteria. However, the studies of bacterial diversity of fermented camel milk are scattered and the amount of available data are still limited. Therefore, it is necessary to explore the microbiota composition and diversity of the traditional fermented camel milk.[Methods] We sequenced the V3-V4 region of 16S rRNA genes in fermented camel milk of Alxa and Sonid Bactrian camel by Illumina Miseq platform, and the microbiota composition and diversity were compared and analyzed.[Results] The results of Alpha diversity showed that the fermented camel milk from Sonid has higher bacterial diversity and microbial community richness than those of Alxa. At the phylum level, Firmicutes and Proteobacteria were dominant in both of them. At the genus level, Lactobacillus and Lactococcus were dominant in Sonid samples, Lactobacillus and Acetobacter were dominant in Alxa samples. In addition, we also found some foodborne pathogens and environmentally contaminating bacteria, such as Enterobacter, Raoultella and Leuconostoc. There were significant differences in the types and dominant bacteria in fermented camel milk in different regions. [Conclusion] These results provide insights into the microbiota community and diversity of traditional fermented camel milk, and also lay the foundation for screening dominant bacteria and excavating new probiotics in the further studies.