Abstract: The main economic trait of swamp buffalo is servitude, while the main economic trait of river buffalo is milk. The difference of host production traits is often accompanied by the change of intestinal microbial community. The metagenomic comparison of the adult river and swamp buffalo gut microbiota was studied in this paper. The results showed that 2 192 526 non-redundant genes were obtained in swamp buffalo and 1 686 914 non-redundant genes were obtained in river buffalo. There were 420 452 non-redundant genes overlapped in the two groups. It could be seen that the number of unique genes of the two kinds of buffalo was much greater than the number of common genes, and there were great differences in the gene composition of gut microbiota. Actinobacteria in swamp buffalo were significantly higher than that in river buffalo. Actinobacteria are the main bacteria in the soil. It was speculated that the swamp buffalo can obtain Actinobacteria by eating fresh grass and contacting closely with the soil in the process of field paddy field servitude. At the genus level, it was found that the relative abundance of Roseburia and Turicibacter in the gut of river buffalo was higher than that of swamp buffalo, and butyric acid and lactate were produced, which provided precursors for the synthesis of meat and milk. It was speculated that it was related to the characteristics of fast growth and the high milk yield of river buffalo. At the species level, Bifidobacterium pseudolongum associated with immunity was found in swamp buffalo gut, Turcibacter＿sanguinis related to lipid metabolism found in river buffalo gut. Further analysis found that the KEGG metabolic pathway network also showed that the lipid metabolism of the intestinal microbiome of river buffalo was more active than that of swamp buffalo, which was related to the high content of buffalo milk fat. In the analysis of the relative abundance of COG functional genes, it was found that the relative abundance of defense mechanisms of gut microbiota of swamp buffalo was higher than that of river buffalo, indicating that swamp buffalo had strong stress resistance. This study preliminarily clarified the similarities and differences of intestinal microbial abundance and function of different types of buffalo, laid a foundation for clarifying the regulation mechanism of intestinal flora structure on buffalo production traits, and also provided an important theoretical reference for improving buffalo economic traits by regulating buffalo intestinal microbial community.