<p>Understanding the bacterial communities in non-vascular plants is essential for revealing the full landscape of plant–microbe interactions. However, comprehensive knowledge about bryophyte-associated bacterial communities remains limited, particularly in subtropical regions. Here, we investigated the bacterial communities of three compartments (soil, phyllosphere, and endosphere) from ten bryophyte species in two subtropical National Nature Reserves using 16S rRNA gene amplicon sequencing. We assessed how host species identity, compartment, and sampling site shape bacterial assembly, function and interactions. Our findings demonstrate that bacterial α diversity, community structure, and predicted functional profiles are influenced by the complex interplay among host species identity, compartment, and sampling site, whereas taxonomic composition and assembly processes are predominantly governed by the compartment. Compared to the soil, the phyllosphere and endosphere communities exhibit a higher proportion of stochastic processes as well as higher clustering coefficients and shorter average path lengths within the networks. Furthermore, taxa more abundant in the endosphere compared to soil exhibit compositional divergence and functional convergence across sites, characterized by higher proportions of terpenoid, polyketide, and xenobiotic metabolism pathways, alongside lower proportions of fundamental biosynthetic pathways. Overall, this study demonstrates that bryophyte-associated bacterial communities are jointly shaped by host species identity, compartment, and environment, and provides key insights into the ecological mechanisms of more extensive plant-microbe interaction patterns.</p>