Aims <p>This study focuses on assessing the diversity and composition of the phyllosphere and rhizosphere communities, exploring the significant overlap in microbial community composition among four different plant functional groups and plant organs, and understanding the fitness match between microorganisms and plants.</p> Methods <p>Sequencing the microorganisms of different plant functional groups (coniferous, broadleaf, shrubs and herbs) and organs (leaves and roots), we obtained the microbial diversity and community structure and analyzed their differences under different environments, with the objective of identifying core groups of microorganisms present across various environmental conditions.</p> Results <p>Across all plant functional groups, bacterial and fungal diversity was higher in the rhizosphere compared to the phyllosphere. Furthermore,&#xa0;bacterial species were more similar in the rhizosphere than in the phyllosphere, suggesting that the leaf surface imposes stronger selective pressures on microbial community composition. The overlap in bacterial and fungal species was higher for herbs compared to taller plant functional groups. This suggests that the similarity in microbial communities between plant organs increases with decreasing plant size. Interestingly, core microbial taxa shared between phyllosphere and rhizosphere were relatively similar for each of the four plant functional groups. Alphaproteobacteria and Dothideomycetes were the dominant taxa in the phyllosphere, whereas Alphaproteobacteria and Agaricomycetes were the dominant taxa in the rhizosphere.</p> Conclusions <p>This study reveals the ubiquity and importance of key microbial taxa within the plant microbiome, highlighting core microorganisms that drive co-evolutionary patterns, while shaping survival, development, and selection across diverse organs and functional groups.</p>