Microorganisms serve important functions within host organisms. An understanding of the variation in plant microbiomes from rhizosphere soils to plant canopies is imperative to gain a better understanding in both the structural and functional processes impacting plant health. Using Populus trees as a model ecosystem, we characterized the archaeal/bacterial and fungal microbiome across 30 different tissue-level niches within Populus deltoides and hybrid Populus trichocarpa x deltoides individuals using 16S and ITS2 rRNA gene Illumina MiSeq sequencing. Our results indicate that archaeal/bacterial and fungal microbiomes varied largely across broad plant habitats (leaves, stems, roots, soils), except for fungal communities within leaves specifically, which were greatly impacted by the host genotype. Archaeal/bacterial diversity increased from leaves to soil habitats, whereas fungal diversity was the greatest in stems and soils. Differences between tree genotypes are evident in the elevated presence of two potential fungal pathogens, Marssonina brunnea and Septoria sp., on hybrid P. trichocarpa x deltoides trees which may in turn be driving divergence in microbiome composition. This study provides a holistic understanding of microbiome structure within a bioenergy relevant plant host. These data allow for further hypothesis testing on the significance of individual microbial taxa within specific plant habitats or plant species.