Populus has been increasingly recognized as an important model tree genus, not only due to its wide distribution around the world and an associated great economic and ecological significance, but also the availability of several poplar genomes. Apart from these advantages, Populus is also an ideal organism for investigating physiological and molecular mechanisms underlying tree-microbe interactions, as poplar trees are able to establish multiple symbiotic relationships with a variety of microorganisms thriving in both above-and belowground tissues. Representative poplar-associated beneficial microbes include ectomycorrhizal fungi, arbuscular mycorrhizal fungi, fungal endophytes, nitrogen-fixing bacteria, and plant-growth-promoting rhizobacteria (PGPR), which generally improve poplar growth, nutrition acquisition, and different types of stress tolerance. Rapid progress has been made in understanding the molecular interactions in the development of ectomycorrhizae in the Laccaria bicolor-poplar system and the mechanisms underlying the ectomycorrhizal fungi-mediated poplar abiotic tolerance. Intriguingly, the ecological significance of mycorrhizal helper bacteria and endohyphal bacterial has been recently appreciated. More importantly, a plant microbiome research project was initiated recently; it extensively revolutionizes our understanding of the structure and functions of plant-associated microbiota. The rhizosphere, endosphere, and phyllosphere microbiomes of several poplar species have been uncovered, indicating that both host genotypes and environmental factors influence the microbial community composition. It has been widely accepted that the rhizosphere and endosphere often harbor distinctive microbiota. Promisingly, the strategy of rhizosphere microbiome engineering will shed light on the contributions that soil microbial communities make in improving tree fitness under stress conditions. Looking forward, it will provide a basis for generating robust microbial inoculants that can be utilized in planting seedlings.