Abstract: Antibiotics not only serve human beings, but also generate new antibiotic resistance genes (ARGs) in other organisms, which seriously endanger the health of human beings and animals. ARGs are widely distributed, and herbivores mainly come into contact with plant microorganisms’ ARGs through feeding. The giant panda (Ailuropoda melanoleuca) has evolved into a bamboo-based diet. The study was conducted in Sichuan Liziping National Nature Reserve, focusing on the composition and diversity of microbial ARGs in the food resources of giant pandas, and using metagenomic sequencing to explore the composition and diversity of giant panda food resources microorganisms ARGs. After analysis, it was found that the ARGs of giant panda’s staple food bamboo phyllosphere bacteria mainly include Tetracycline, MLS (macrolide lincomycin streptomycin), Glycopeptides and Peptides at the class level. The Sobs index of ARGs around the leaves of Arundinaria spanostachya was significantly higher than that of Fargesia ferax. However, there was no significant difference in the Shannon index among the three bamboo species. Further analysis by NMDS revealed significant differences in the composition and structure of ARGs among the three main food sources of giant pandas. Through LEfSe analysis, important species of phyllosphere bacteria ARGs were identified to distinguish the three main food sources of giant pandas. Glycopeptide, Phenol, and Bicyclomycin played the most important role in Arundinaria spanostachya. Aminocoumarin and Pleurocutilin played the most important roles in the Fargesia ferax. Glycopeptide and Phenol were mainly carried by Pseudomonas and Sphingomonas, while Aminocoumarin and Pleurocutilin were mainly carried by Sphingomonas and Lichenibacterium. This study suggests that the bamboo phyllosphere microbiota consumed by giant pandas contain abundant ARGs. And in daily monitoring, it is necessary to focus on monitoring the most important bacterial groups (such as Pseudomonas, Sphingomonas, etc.), which are distinguishing the antibiotic resistance genes among the three giant panda’s staple food bamboo phyllosphere bacteria. In addition, it is necessary to pay attention to the status of microbial ARGs in other environments (soil, streams, trees, etc.) in order to comprehensively understand the potential impact of environmental microorganisms and their ARGs on giant pandas.