Abstract The cross-species transmission of intestinal bacteria caused by mixed-group contact in animals is currently an issue of concern. Herring gulls (Larus argentatus) and common shelducks (Tadorna tadorna) often forage in mixed groups, a process which is known as sympatric mixed foraging. This study sought to explore how mixed foraging affects the gut bacteria structure in herring gulls and common shelducks on Binzhou Seashell Island, China. Illumina high-throughput sequencing was employed to analyze the intestinal bacteria of these birds during their wintering period, with the goal of understanding the impact of mixed-species interactions on gut microbiota diversity. The results showed that alpha diversity of intestinal flora in common shelducks was higher than that in herring gulls, and there was no significant difference in beta diversity between the two species. The similarity ratio of the top five abundances of bacteria at the phylum classification level reached 42.86%. Judging from the results, there is resemblance in the structure of the intestinal flora between the two species. The study not only enhances our understanding of the adaptive strategies and interactions of these two avian species within the ecosystem, but also establishes a crucial foundation for bird resource management and disease prevention and control in this region. It holds significant scientific and practical implications for fields such as ecological conservation and biodiversity.