Background <p>Mango is an economically important fruit tree with rich genetic diversity, but has been threatened by a diverse range of pathogens, causing substantial losses annually. While the plant-associated microbiomes are well studied, the assembly patterns and composition of phyllosphere microbial communities for deciphering potential pathogenic and beneficial microbiota during the mango fruit-setting phase remain largely unexplored.</p> Results <p>This study profiled the bacterial and fungal communities in mango leaves, flowers, and fruitlets using high-throughput amplicon sequencing. Both flowers and fruitlets exhibited significantly less diverse microbial communities than leaves, and the bacterial and fungal microbiota compositions of all three organs were distinct from one another. Importantly, organ-specific preferences were observed among the dominant bacterial families, with mango flowers characterized by a high abundance of Erwiniaceae, fruitlets by Acetobacteraceae, and leaves by Microbacteriaceae and Bifidobacteriaceae. In contrast, fungal families were less differentiated, with only Didymellaceae and Symmetrosporaceae showing leaf-specific enrichment relative to flowers and fruitlets. Analysis of the shared microbial genera across the three phyllosphere organs revealed the presence of core bacterial taxa <i>Pseudomonas</i> and <i>Sphingomonas</i>, while the fungal core genera were <i>Alternaria</i>, <i>Aureobasidium</i>, <i>Cladosporium</i>, <i>Epicoccum</i>, <i>Fusarium</i>, <i>Hannaella</i>, <i>Nectria</i>, <i>Neodidymella</i>, and <i>Vishniacozyma</i>. Notably, several of these concurrently detected microbial genera have been previously documented as either pathogenic (e.g., <i>Alternaria</i>, <i>Cladosporium</i> and <i>Fusarium</i>) or beneficial (<i>Aureobasidium</i>, <i>Vishniacozyma</i>,<i> Sphingomonas</i> and <i>Pseudomonas</i>). Furthermore, we found that the mango phyllosphere bacterial and fungal communities were established by parallel selection of the microbiota, instead of consecutive selection. Deciphering the functional profile of the phyllosphere microbiota revealed the association of microbial taxa with functions such as chemoheterotrophy, aerobic chemoheterotrophy, fermentation, aromatic compound degradation, plant pathogens, endophytes, and saprotrophs, indicating a balanced ecosystem in which future fruit health outcomes may be determined by subtle shifts in the microbial community structure.</p> Conclusion <p>Our findings offer a checklist of the core beneficial and pathogenic microbes inhabiting the mango phyllosphere, while also highlighting the selective role of mango organs in recruiting specific subsets of microbiota, which can be harnessed for disease protection and improving mango production.</p>