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The microbial diversity in Bactrian camel milk and naturally fermented camel milk with unique nutritional properties and medicinal value in Alxa, Inner Mongolia, has been little reported. The results of this study showed that the dominant bacterial phyla in Bactrian camel milk and naturally fermented camel milk were Firmicutes and Proteobacteria, and dominant fungal phyla were Ascomycota and Basidiomycota. During the natural fermentation process of Bactrian camel milk, dominant bacterial genus changed from Lactococcus to Lactobacillus , while dominant fungal genera changed from Apiotrichum , Cutaneotrichosporon and Candida to Kazachstania and Kluyveromyces. Therefore, the diversity and flora structure of bacteria and fungi in Bactrian camel milk and naturally fermented camel milk were significantly different (P < 0.05). The predicted gene functions by PICRUSt2 software showed that the main metabolic genes of bacteria were global and overview maps, carbohydrate metabolism and amino acid metabolism, etc.; the main metabolic genes of fungi were glyoxylate cycle, aerobic respiration I and II, etc. And the relative abundance of bacteria related to food-borne pathogenicity and environmental pollution such as Enterobacter , Enterococcus and Raoultella , etc. suddenly decreased, which provides a reference for the safety evaluation of camel milk and camel milk products and a basis for the study of probiotics. • The microbial diversity of Bactrian camel milk and fermented camel milk was revealed. • Changes of microbial communities in Bactrian camel milk during natural fermentation. • Changes in genera of food-borne pathogenicity and environmental bacteria. • KEGG analysis showed the main metabolic pathways of bacteria and fungi. • To provide reference for safety evaluation of camel milk and camel milk products. [ABSTRACT FROM AUTHOR]