Abstract: Fruit trees, vital to global agriculture, depend heavily on pollinators to facilitate successful reproduction and ensure optimal yield. Microorganisms associated with anthers can influence pollen viability, and their community composition may be affected by pollinator activity. While understanding the diversity and community assembly patterns of these microorganisms has potential implications for enhancing the reproductive fitness of fruit trees, research in this area remains relatively scarce. This study employed high-throughput sequencing to analyze the diversity and community structure of fungi and bacteria on the anthers of loquat (Eriobotrya japonica (Thunb.) Lindl.) before (bagged group) and after (nature group) pollinator visitation. Results showed that pollinator visitation had no significant effect on the diversity or composition of anther microbiomes. In the bagged group, dominant fungal taxa included Cladosporiaceae and Mycosphaerellaceae, whereas Cladosporiaceae and Metschnikowiaceae were dominant in the nature group. Bacterial communities in both groups were also dominated by Alcaligenaceae and Erwiniaceae. These findings indicate that the microbial community composition within loquat anthers is inherently stable and largely unaffected by pollinator activity.