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Endophytes asymptomatically infect virtually all plant species, yet little is known about endophyte community assembly and diversity within the woody tissues of forest trees. We utilised phylogenetic null models of alpha (ses.MNTD_ab and ses.MPD_ab) and beta diversity (ses.ßMNTD_ab and ses.ßMPD_ab) to infer the role of deterministic and stochastic ecological processes in structuring bacterial and fungal endophyte communities in the woody tissues of Populus deltoides and the naturally occurring P. × jackii hybrid complex (P. deltoides × P. balsamifera). Microbial communities were characterised through Illumina amplicon sequencing (MiSeq) of the ITS and 16S rRNA gene. We detected 227 fungal ASVs, which were mainly classified as Ascomycota (92.4%). Among the 667 bacterial ASVs detected, the majority were classified as phylum Actinobacteriota (47.6%) and Proteobacteria (44.9%). We predicted that hybridisation could lead to a host environment that applies weaker selective effects on microbial taxa due to variability in host chemical and morphological phenotypes. Although bacterial communities did not support our prediction, fungal assemblages of the hybrid host (P. × jackii) were more phylogenetically random within (ses.MNTD_ab) and between assemblages (ses.ßMNTD_ab and ses.ßMPD_ab) then the non-hybrid (P. deltoides)-consistent with an increased role of stochastic community assembly processes and less selective host environment. Host identity had a large influence on fungal community composition (weighted UniFrac R² = 34%), which may result from the differences in fungal selection we detected between hosts. Conversely, host identity was a weaker predictor of bacterial composition (weighted UniFrac R² = 13%), which may reflect the more dominant role of stochasticity we detected in bacterial assembly. Our findings provide evidence that host hybridisation may alter fungal assembly processes and diversity within the woody endosphere, leading to more phylogenetically diverse associations both within and between the fungal assemblages of hybrid trees. More broadly, our results highlight how genetically diverse host populations may promote microbial biodiversity within forests and hybrid transition zones.